Single-strand Specificity of APOBEC3G Accounts for Minus-strand Deamination of the HIV Genome

Nature Structural & Molecular Biology. May, 2004  |  Pubmed ID: 15098018

HIV-1 deleted for the vif accessory gene encapsidates the cellular cytidine deaminase APOBEC3G. Upon infection, the encapsidated APOBEC3G induces G-->A mutations in the viral reverse transcripts. The G-->A mutations result either from C-->U deamination of the minus strand or deamination of both strands followed by repair of the plus strand. We report here that minus-strand deamination occurred over the length of the virus genome, preferentially at CCCA sequences, with a graded frequency in the 5'-->3' direction. APOBEC3G induced previously undetected C-->T mutations in the 5' U3 and the primer-binding site, both of which become transiently single-stranded during reverse transcription. In vitro, APOBEC3G bound and deaminated single-stranded DNA (ssDNA) but not double-stranded DNA (dsDNA) or DNA-RNA hybrids. We propose that the requirement for ssDNA accounts for the minus-strand mutations, the 5'-->3' graded frequency of deamination and the rare C-->T mutations.

Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-experienced Patients Are Missed by Standard Genotype Analysis

Journal of Clinical Microbiology. Jan, 2005  |  Pubmed ID: 15635002

To investigate the extent to which drug resistance mutations are missed by standard genotyping methods, we analyzed the same plasma samples from 26 patients with suspected multidrug-resistant human immunodeficiency virus type 1 by using a newly developed single-genome sequencing technique and compared it to standard genotype analysis. Plasma samples were obtained from patients with prior exposure to at least two antiretroviral drug classes and who were on a failing antiretroviral regimen. Standard genotypes were obtained by reverse transcriptase (RT)-PCR and sequencing of the bulk PCR product. For single-genome sequencing, cDNA derived from plasma RNA was serially diluted to 1 copy per reaction, and a region encompassing p6, protease, and a portion of RT was amplified and sequenced. Sequences from 15 to 46 single viral genomes were obtained from each plasma sample. Drug resistance mutations identified by single-genome sequencing were not detected by standard genotype analysis in 24 of the 26 patients studied. Mutations present in less than 10% of single genomes were almost never detected in standard genotypes (1 of 86). Similarly, mutations present in 10 to 35% of single genomes were detected only 25% of the time in standard genotypes. For example, in one patient, 10 mutations identified by single-genome sequencing and conferring resistance to protease inhibitors (PIs), nucleoside analog reverse transcriptase inhibitors, and nonnucleoside reverse transcriptase inhibitors (NNRTIs) were not detected by standard genotyping methods. Each of these mutations was present in 5 to 20% of the 20 genomes analyzed; 15% of the genomes in this sample contained linked PI mutations, none of which were present in the standard genotype. In another patient sample, 33% of genomes contained five linked NNRTI resistance mutations, none of which were detected by standard genotype analysis. These findings illustrate the inadequacy of the standard genotype for detecting low-frequency drug resistance mutations. In addition to having greater sensitivity, single-genome sequencing identifies linked mutations that confer high-level drug resistance. Such linkage cannot be detected by standard genotype analysis.

Selection and Persistence of Non-nucleoside Reverse Transcriptase Inhibitor-resistant HIV-1 in Patients Starting and Stopping Non-nucleoside Therapy

AIDS (London, England). Mar, 2006  |  Pubmed ID: 16514300

Understanding the selection and decay of drug-resistant HIV-1 variants is important for designing optimal antiretroviral therapy.

Blinded, Multicenter Comparison of Methods to Detect a Drug-resistant Mutant of Human Immunodeficiency Virus Type 1 at Low Frequency

Journal of Clinical Microbiology. Jul, 2006  |  Pubmed ID: 16825395

We determined the abilities of 10 technologies to detect and quantify a common drug-resistant mutant of human immunodeficiency virus type 1 (lysine to asparagine at codon 103 of the reverse transcriptase) using a blinded test panel containing mutant-wild-type mixtures ranging from 0.01% to 100% mutant. Two technologies, allele-specific reverse transcriptase PCR and a Ty1HRT yeast system, could quantify the mutant down to 0.1 to 0.4%. These technologies should help define the impact of low-frequency drug-resistant mutants on response to antiretroviral therapy.

Suppression of Viremia and Evolution of Human Immunodeficiency Virus Type 1 Drug Resistance in a Macaque Model for Antiretroviral Therapy

Journal of Virology. Nov, 2007  |  Pubmed ID: 17855539

Antiretroviral therapy (ART) in human immunodeficiency virus type 1 (HIV-1)-infected patients does not clear the infection and can select for drug resistance over time. Not only is drug-resistant HIV-1 a concern for infected individuals on continual therapy, but it is an emerging problem in resource-limited settings where, in efforts to stem mother-to-child-transmission of HIV-1, transient nonnucleoside reverse transcriptase inhibitor (NNRTI) therapy given during labor can select for NNRTI resistance in both mother and child. Questions of HIV-1 persistence and drug resistance are highly amenable to exploration within animals models, where therapy manipulation is less constrained. We examined a pigtail macaque infection model responsive to anti-HIV-1 therapy to study the development of resistance. Pigtail macaques were infected with a pathogenic simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT-SHIV) to examine the impact of prior exposure to a NNRTI on subsequent ART comprised of a NNRTI and two nucleoside RT inhibitors. K103N resistance-conferring mutations in RT rapidly accumulated in 2/3 infected animals after NNRTI monotherapy and contributed to virologic failure during ART in 1/3 animals. By contrast, ART effectively suppressed RT-SHIV in 5/6 animals. These data indicate that suboptimal therapy facilitates HIV-1 drug resistance and suggest that this model can be used to investigate persisting viral reservoirs.

Frequent Polymorphism at Drug Resistance Sites in HIV-1 Protease and Reverse Transcriptase

AIDS (London, England). Feb, 2008  |  Pubmed ID: 18301062

Failure of antiretroviral therapy may result from the selection of pre-existing, drug-resistant HIV-1 variants, but the frequency and type of such variants have not been defined.

Modelling the Impact of Antibiotic Use and Infection Control Practices on the Incidence of Hospital-acquired Methicillin-resistant Staphylococcus Aureus: a Time-series Analysis

The Journal of Antimicrobial Chemotherapy. Sep, 2008  |  Pubmed ID: 18467307

Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen worldwide. A wide range of factors have been suggested to influence the spread of MRSA. The objective of this study was to evaluate the effect of antimicrobial drug use and infection control practices on nosocomial MRSA incidence in a 426-bed general teaching hospital in Northern Ireland.

Comparison of the Effect of Ciprofloxacin and Tazocin on the Incidence of Meticillin-resistant Staphylococcus Aureus (MRSA) in an Intensive Care Unit

International Journal of Antimicrobial Agents. Dec, 2008  |  Pubmed ID: 18801646

Meticillin-resistant Staphylococcus aureus (MRSA) is a very significant agent of recalcitrant healthcare-associated infections. A major risk of acquiring such infections is thought to be modulated by the use of particular antimicrobial therapies. The aim of this research was to evaluate prospectively the impact of using either ciprofloxacin or Tazocin (piperacillin+tazobactam) on the incidence of MRSA in an Intensive Care Unit (ICU). The 1-year (2 x 6 months) cross-over study was carried out in a medium-sized (426 beds) teaching hospital. During the first 6-month period, ciprofloxacin was used as the first-line broad-spectrum antibiotic therapy of choice. During the second 6-month period, Tazocin was used as first-line therapy. The incidence of hospital-acquired MRSA (i.e. colonised and/or infected) and rates of compliance of the ICU healthcare workers to optimal hand hygiene practices were recorded throughout the study. The study observed no statistically significant differences (P = 0.1) between MRSA incidence rates in the ICU during the ciprofloxacin (4.4/1000 bed-days) or Tazocin (11.4/1000 bed-days) arms of the study. Interestingly, observing healthcare workers' hand hygiene practices throughout the entire study showed that healthcare workers adhered to these practices 59.2% of the time during the ciprofloxacin arm and 66.0% during the Tazocin arm. The low incidence rates within the unit demonstrated the importance of infection control in limiting the spread of MRSA despite the extensive use of antibiotics in a high-risk setting.

Evaluation of the Efficacy of a Conventional Cleaning Regimen in Removing Methicillin-resistant Staphylococcus Aureus from Contaminated Surfaces in an Intensive Care Unit

Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America. Mar, 2009  |  Pubmed ID: 19215198

Quasiexperimental Study of the Effects of Antibiotic Use, Gastric Acid-suppressive Agents, and Infection Control Practices on the Incidence of Clostridium Difficile-associated Diarrhea in Hospitalized Patients

Antimicrobial Agents and Chemotherapy. May, 2009  |  Pubmed ID: 19289520

The objective of this study was to evaluate the effects of antimicrobial drug use, gastric acid-suppressive agent use, and infection control practices on the incidence of Clostridium difficile-associated diarrhea (CDAD) in a 426-bed general teaching hospital in Northern Ireland. The study was retrospective and ecological in design. A multivariate autoregressive integrated moving average (time-series analysis) model was built to relate CDAD incidence with antibiotic use, gastric acid-suppressive agent use, and infection control practices within the hospital over a 5-year period (February 2002 to March 2007). The findings of this study showed that temporal variation in CDAD incidence followed temporal variations in expanded-spectrum cephalosporin use (average delay = 2 months; variation of CDAD incidence = 0.01/100 bed-days), broad-spectrum cephalosporin use (average delay = 2 months; variation of CDAD incidence = 0.02/100 bed-days), fluoroquinolone use (average delay = 3 months; variation of CDAD incidence = 0.004/100 bed-days), amoxicillin-clavulanic acid use (average delay = 1 month; variation of CDAD incidence = 0.002/100 bed-days), and macrolide use (average delay = 5 months; variation of CDAD incidence = 0.002/100 bed-days). Temporal relationships were also observed between CDAD incidence and use of histamine-2 receptor antagonists (H2RAs; average delay = 1 month; variation of CDAD incidence = 0.001/100 bed-days). The model explained 78% of the variance in the monthly incidence of CDAD. The findings of this study highlight a temporal relationship between certain classes of antibiotics, H2RAs, and CDAD incidence. The results of this research can help hospitals to set priorities for restricting the use of specific antibiotic classes, based on the size-effect of each class and the delay necessary to observe an effect.

Prevalence of Methicillin-resistant Staphylococcus Aureus Colonization in Residents and Staff in Nursing Homes in Northern Ireland

Journal of the American Geriatrics Society. Apr, 2009  |  Pubmed ID: 19392953

To determine the prevalence of, and factors associated with, methicillin-resistant Staphylococcus aureus (MRSA) colonization in residents and staff in nursing homes in one geographically defined health administration area of Northern Ireland.

Health-related Quality of Life After Intensive Care Unit Discharge: A Comparison Between 2 Standard Antibiotic Regimens

Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America. Aug, 2009  |  Pubmed ID: 19591584

An Evaluation of Compliance with an Antibiotic Policy in Surgical Wards at a General Teaching Hospital in Northern Ireland

Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America. Sep, 2009  |  Pubmed ID: 19653821

Antioxidants and Other Pharmacological Treatments for Friedreich Ataxia

Cochrane Database of Systematic Reviews (Online). 2009  |  Pubmed ID: 19821439

Friedreich ataxia is a rare inherited, autosomal recessive, neurological disorder characterised initially by unsteadiness in standing and walking, slowly progressing to wheelchair dependency usually in the late teens or early twenties. It is associated with slurred speech, scoliosis, pes cavus and heart abnormalities which may cause premature death in 60 to 80% of people. There is no easily defined clinical or biochemical marker and no known treatment.

RT-SHIV Subpopulation Dynamics in Infected Macaques During Anti-HIV Therapy

Retrovirology. 2009  |  Pubmed ID: 19889213

To study the dynamics of wild-type and drug-resistant HIV-1 RT variants, we developed a methodology that follows the fates of individual genomes over time within the viral quasispecies. Single genome sequences were obtained from 3 pigtail macaques infected with a recombinant simian immunodeficiency virus containing the RT coding region from HIV-1 (RT-SHIV) and treated with short-course efavirenz monotherapy 13 weeks post-infection followed by daily combination antiretroviral therapy (ART) beginning at week 17. Bioinformatics tools were constructed to trace individual genomes from the beginning of infection to the end of the treatment.

Low Frequency Nonnucleoside Reverse-transcriptase Inhibitor-resistant Variants Contribute to Failure of Efavirenz-containing Regimens in Treatment- Experienced Patients

The Journal of Infectious Diseases. Mar, 2010  |  Pubmed ID: 20102272

The contribution of low frequency drug-resistant human immunodeficiency virus type 1 (HIV-1) variants to failure of antiretroviral therapy is not well defined in treatment-experienced patients. We sought to detect minor nonnucleoside reverse-transcriptase inhibitor (NNRTI)-resistant variants at the initiation of multidrug efavirenz-containing therapy in both NNRTI-naive and NNRTI-experienced patients and to determine their association with virologic response.

Comparison of Standard PCR/cloning to Single Genome Sequencing for Analysis of HIV-1 Populations

Journal of Virological Methods. Sep, 2010  |  Pubmed ID: 20451557

To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naïve patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity.

Patterns of Human Immunodeficiency Virus Type 1 Recombination Ex Vivo Provide Evidence for Coadaptation of Distant Sites, Resulting in Purifying Selection for Intersubtype Recombinants During Replication

Journal of Virology. Aug, 2010  |  Pubmed ID: 20504919

High-frequency recombination is a hallmark of HIV-1 replication. Recombination can occur between two members of the same subtype or between viruses from two different subtypes, generating intra- or intersubtype recombinants, respectively. Many intersubtype recombinants have been shown to circulate in human populations. We hypothesize that sequence diversity affects the emergence of viable recombinants by decreasing recombination events and reducing the ability of the recombinants to replicate. To test our hypothesis, we compared recombination between two viruses containing subtype B pol genes (B/B) and between viruses with pol genes from subtype B or F (B/F). Recombination events generated during a single cycle of infection without selection pressure on pol gene function were analyzed by single-genome sequencing. We found that recombination occurred slightly ( approximately 30%) less frequently in B/F than in B/B viruses, and the overall distribution of crossover junctions in pol was similar for the two classes of recombinants. We then examined the emergence of recombinants in a multiple cycle assay, so that functional pol gene products were selected. We found that the emerging B/B recombinants had complex patterns, and the crossover junctions were distributed throughout the pol gene. In contrast, selected B/F recombinants had limited recombination patterns and restricted crossover junction distribution. These results provide evidence for the evolved coadapted sites in variants from different subtypes; these sites may be segregated by recombination events, causing the newly generated intersubtype recombinants to undergo purifying selection. Therefore, the ability of the recombinants to replicate is the major barrier for many of these viruses.

The Effect of Raltegravir Intensification on Low-level Residual Viremia in HIV-infected Patients on Antiretroviral Therapy: a Randomized Controlled Trial

PLoS Medicine. 2010  |  Pubmed ID: 20711481

Most HIV-1-infected patients on effective antiretroviral therapy (ART) with plasma HIV-1 RNA levels below the detection limits of commercial assays have residual viremia measurable by more sensitive methods. We assessed whether adding raltegravir lowered the level of residual viremia in such patients.

HIV-1 Continues to Replicate and Evolve in Patients with Natural Control of HIV Infection

Journal of Virology. Dec, 2010  |  Pubmed ID: 20926564

Elucidating mechanisms leading to the natural control of HIV-1 infection is of great importance for vaccine design and for understanding viral pathogenesis. Rare HIV-1-infected individuals, termed HIV-1 controllers, have plasma HIV-1 RNA levels below the limit of detection by standard clinical assays (<50 to 75 copies/ml) without antiretroviral therapy. Although several recent studies have documented persistent low-grade viremia in HIV-1 controllers at a level not significantly different from that in HIV-1-infected individuals undergoing treatment with combination antiretroviral therapy (cART), it is unclear if plasma viruses are undergoing full cycles of replication in vivo or if the infection of new cells is completely blocked by host immune mechanisms. We studied a cohort of 21 HIV-1 controllers with a median level of viremia below 1 copy/ml, followed for a median of 11 years. Less than half of the cohort carried known protective HLA types (B*57/27). By isolating HIV-1 RNA from large volumes of plasma, we amplified single genome sequences of both pro-rt and env longitudinally. This study is the first to document that HIV-1 pro-rt and env evolve in this patient group, albeit at rates somewhat lower than in HIV-1 noncontrollers, in HLA B*57/27-positive, as well as HLA B*57/27-negative, individuals. Viral diversity and adaptive events associated with immune escape were found to be restricted in HIV-1 controllers, suggesting that replication occurs in the face of less overall immune selection.

Current Status of Xenotropic Murine Leukemia Virus-related Retrovirus in Chronic Fatigue Syndrome and Prostate Cancer: Reach for a Scorecard, Not a Prescription Pad

The Journal of Infectious Diseases. Nov, 2010  |  Pubmed ID: 20936981

Genetic Diversity of Simian Immunodeficiency Virus Encoding HIV-1 Reverse Transcriptase Persists in Macaques Despite Antiretroviral Therapy

Journal of Virology. Jan, 2011  |  Pubmed ID: 21084490

The impact of antiretroviral therapy (ART) on the genetics of simian immunodeficiency virus (SIV) or human immunodeficiency virus (HIV) populations has been incompletely characterized. We analyzed SIV genetic variation before, during, and after ART in a macaque model. Six pigtail macaques were infected with an SIV/HIV chimeric virus, RT-SHIV(mne), in which SIV reverse transcriptase (RT) was replaced by HIV-1 RT. Three animals received a short course of efavirenz (EFV) monotherapy before combination ART was started. All macaques received 20 weeks of tenofovir, emtricitabine, and EFV. Plasma virus populations were analyzed by single-genome sequencing. Population diversity was measured by average pairwise difference, and changes in viral genetics were assessed by phylogenetic and panmixia analyses. After 20 weeks of ART, viral diversity was not different from pretherapy viral diversity despite more than 10,000-fold declines in viremia, indicating that, within this range, there is no relationship between diversity and plasma viremia. In two animals with consistent SIV RNA suppression to <15 copies/ml during ART, there was no evidence of viral evolution. In contrast, in the four macaques with viremias >15 copies/ml during therapy, there was divergence between pre- and during-ART virus populations. Drug resistance mutations emerged in two of these four animals, resulting in virologic failure in the animal with the highest level of pretherapy viremia. Taken together, these findings indicate that viral diversity does not decrease with suppressive ART, that ongoing replication occurs with viremias >15 copies/ml, and that in this macaque model of ART drug resistance likely emerges as a result of incomplete suppression and preexisting drug resistance mutations.

A Point Prevalence Survey of Antibiotic Prescriptions: Benchmarking and Patterns of Use

British Journal of Clinical Pharmacology. Feb, 2011  |  Pubmed ID: 21219412

The aim of the study was to assess current patterns of antibiotic prescribing and the impact of a hospital antibiotic policy on these practices.

Estimate of Effective Recombination Rate and Average Selection Coefficient for HIV in Chronic Infection

Proceedings of the National Academy of Sciences of the United States of America. Apr, 2011  |  Pubmed ID: 21436045

HIV adaptation to a host in chronic infection is simulated by means of a Monte-Carlo algorithm that includes the evolutionary factors of mutation, positive selection with varying strength among sites, random genetic drift, linkage, and recombination. By comparing two sensitive measures of linkage disequilibrium (LD) and the number of diverse sites measured in simulation to patient data from one-time samples of pol gene obtained by single-genome sequencing from representative untreated patients, we estimate the effective recombination rate and the average selection coefficient to be on the order of 1% per genome per generation (10(-5) per base per generation) and 0.5%, respectively. The adaptation rate is twofold higher and fourfold lower than predicted in the absence of recombination and in the limit of very frequent recombination, respectively. The level of LD and the number of diverse sites observed in data also range between the values predicted in simulation for these two limiting cases. These results demonstrate the critical importance of finite population size, linkage, and recombination in HIV evolution.

Multihospital Outbreak of Clostridium Difficile Ribotype 027 Infection: Epidemiology and Analysis of Control Measures

Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America. Mar, 2011  |  Pubmed ID: 21460505

To report a large outbreak of Clostridium difficile infection (CDI; ribotype 027) between June 2007 and August 2008, describe infection control measures, and evaluate the impact of restricting the use of fluoroquinolones in controlling the outbreak.

An Evaluation of the Impact of a Single-dose Intravenous Immunoglobulin Regimen in the Treatment of Clostridium Difficile Infections

Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America. Jun, 2011  |  Pubmed ID: 21558782

Majority of CD4+ T Cells from Peripheral Blood of HIV-1-infected Individuals Contain Only One HIV DNA Molecule

Proceedings of the National Academy of Sciences of the United States of America. Jul, 2011  |  Pubmed ID: 21690402

Neither the number of HIV-1 proviruses within individual infected cells in HIV-1-infected patients nor their genetic relatedness within individual infected cells and between cells and plasma virus are well defined. To address these issues we developed a technique to quantify and genetically characterize HIV-1 DNA from single infected cells in vivo. Analysis of peripheral blood CD4(+) T cells from nine patients revealed that the majority of infected cells contain only one copy of HIV-1 DNA, implying a limited potential for recombination in virus produced by these cells. The genetic similarity between HIV populations in CD4(+) T cells and plasma implies ongoing exchange between these compartments both early and late after infection.

Failure to Confirm XMRV/MLVs in the Blood of Patients with Chronic Fatigue Syndrome: a Multi-laboratory Study

Science (New York, N.Y.). Nov, 2011  |  Pubmed ID: 21940862

Murine leukemia viruses (MLVs), including xenotropic-MLV-related virus (XMRV), have been controversially linked to chronic fatigue syndrome (CFS). To explore this issue in greater depth, we compiled coded replicate samples of blood from 15 subjects previously reported to be XMRV/MLV-positive (14 with CFS) and from 15 healthy donors previously determined to be negative for the viruses. These samples were distributed in a blinded fashion to nine laboratories, which performed assays designed to detect XMRV/MLV nucleic acid, virus replication, and antibody. Only two laboratories reported evidence of XMRV/MLVs; however, replicate sample results showed disagreement, and reactivity was similar among CFS subjects and negative controls. These results indicate that current assays do not reproducibly detect XMRV/MLV in blood samples and that blood donor screening is not warranted.

The Impact of Antibiotic Use on the Incidence and Resistance Pattern of ESBL-producing Bacteria in Primary and Secondary Healthcare Settings

British Journal of Clinical Pharmacology. Dec, 2011  |  Pubmed ID: 22150975

What is already known about this subject - The emergence and spread of bacteria producing extended-spectrum beta-lactamases (ESBLs) has important therapeutic and epidemiologic implications. - A key target for the establishment of hospital antibiotic stewardship is reducing the occurrence of additional antibiotic resistance. - Further research is needed to accumulate supporting evidence that reducing antibiotic use will result in a parallel reduction in antibiotic resistance What this study adds - Fluoroquinolone restriction reverses ciprofloxacin resistance in primary and secondary healthcare settings. - Fluoroquinolone restriction reduced ESBL-producing bacteria incidence rates in both the primary and secondary healthcare settings - Highlights the value of time-series analysis in designing efficient antibiotic stewardship. Background: the objective of the present study was to study the relationship between hospital antibiotic use, community antibiotic use, and the incidence of extended-spectrum beta-lactamase (ESBL)-producing bacteria in hospitals, while assessing the impact of a fluoroquinolone restriction policy on ESBL-producing bacteria incidence rates. Methods: the study was retrospective and ecological in design. A multivariate autoregressive integrated moving average (ARIMA) model was built to relate antibiotic use to ESBLs incidence rates and resistance patterns over a five-year period (January 2005- December 2009). Results: Analysis showed that hospital incidence of ESBLs had a positive relationship with the use of fluoroquinolones in the hospital (coefficient = 0.174, p = 0.02), amoxicillin-clavulanic acid in the community (coefficient = 1.03, p = 0.03), and mean co-morbidity scores for hospitalised patients (coefficient = 2.15, p = 0.03) with various time lags. The fluoroquinolone restriction policy was implemented successfully with the mean use of fluoroquinolones (mainly ciprofloxacin) being reduced from 133 to 17 define daily doses (DDDs)/1000 bed-days (p < 0.001) and from 0.65 to 0.54 DDDs/1000 (p = 0.0007) inhabitants per day, in both the hospital and its surrounding community, respectively. This was associated with an improved ciprofloxacin-susceptibility in both settings [ciprofloxacin-susceptibility being improved from 16% to 28% in the community (p < 0.001)], and with a statistically significant reduction in ESBL-producing bacteria incidence rates. Discussion: This study supports the value of restricting the use of certain antimicrobial classes to control ESBL, and demonstrate the feasibility of reversing resistance patterns post successful antibiotic restriction. The study also highlights the potential value of the time-series analysis in designing efficient antibiotic stewardship.

Restricted Replication of Xenotropic Murine Leukemia Virus-Related Virus in Pigtailed Macaques

Journal of Virology. Jan, 2012  |  Pubmed ID: 22238316

Although Xenotropic Murine Leukemia Virus-related Virus (XMRV) has been previously linked to prostate cancer and myalgic encephalomyelitis/chronic fatigue syndrome, recent data indicate that results interpreted as evidence of human XMRV infection reflect laboratory contamination rather than authentic in vivo infection. Nevertheless, XMRV is a retrovirus of undefined pathogenic potential, able to replicate in human cells. Here, we describe comprehensive analysis of two male pigtailed macaques (Macaca nemestrina) experimentally infected with XMRV. Following intravenous inoculation with >10(10) RNA copy equivalents of XMRV, viral replication was limited and transient, peaking at ≤2200 viral RNA (vRNA) copies/ml plasma and becoming undetectable by 4 weeks postinfection, though viral DNA (vDNA) in PBMC remained detectable through 119 days of follow-up. Similarly, vRNA was not detectable in LN by in situ hybridization (ISH) despite detectable vDNA. Sequencing of cell-associated vDNA revealed extensive G-to-A hypermutation, suggestive of APOBEC-mediated viral restriction. Consistent with limited viral replication, we found transient upregulation of type I IFN responses that returned to baseline by 2 weeks postinfection, no detectable cellular immune responses, and limited or no spread to prostate tissue. Antibody responses, including neutralizing antibodies, however, were detectable by 2 weeks postinfection and maintained throughout the study. Both animals were healthy for the duration of follow-up. These findings indicate that XMRV replication and spread were limited in pigtailed macaques, predominantly by APOBEC-mediated hypermutation. Given that human APOBEC proteins restrict XMRV infection in vitro, human XMRV infection, if it occurred, would be expected to be characterized by similarly limited viral replication and spread.

No Effect of Raltegravir Intensification on Viral Replication Markers in the Blood of HIV-1-Infected Patients Receiving Antiretroviral Therapy

Journal of Acquired Immune Deficiency Syndromes (1999). Mar, 2012  |  Pubmed ID: 22083073

BACKGROUND:: Controversy continues regarding the extent of ongoing viral replication in HIV-1-infected patients on effective antiretroviral therapy (ART). Adding an additional potent agent, such as raltegravir, to effective ART in patients with low-level residual viremia may reveal whether there is ongoing HIV-1 replication. METHODS:: We previously reported the outcome of a randomized placebo-controlled study of raltegravir intensification in patients on ART with HIV-1 RNA <50 copies per milliliter that showed no effect on residual viremia measured by single copy assay. We now report the effects of raltegravir intensification in that trial on other potential measures of ongoing HIV-1 replication as follows: 2-LTR HIV-1 circles, total cellular HIV-1 DNA, and T-cell activation. RESULTS:: Of 50 patients tested, 12 (24%) had 2-LTR circles detected at baseline. Patients who were 2-LTR-positive had higher plasma HIV-1 RNA and HIV-1 DNA levels than 2-LTR-negative individuals. At week 12 of raltegravir intensification, there was no change from baseline in 2-LTR circles, in total HIV-1 DNA or in the ratio of 2-LTR circles to total HIV-1 DNA. There was also no change in markers of T-cell activation. CONCLUSIONS:: In HIV-1-infected individuals on effective ART, we find no evidence of ongoing viral replication in the blood that is suppressible by raltegravir intensification. The results imply that raltegravir intensification alone will not eradicate HIV-1 infection.