Journal: The Journal of Infectious Diseases

Abbreviation

J Infect Dis

Publisher

Oxford University Press

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ISSN

0022-1899
1537-6613

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Publications 1 - 10 of 17
  • Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology
    Item type: Journal Article
    Vasylyeva, Tetyana I.; Du Plessis, Louis; Pineda-Peña, Andrea C.; et al. (2019)
    The Journal of Infectious Diseases
    Background Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. Methods Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups. Results We identified 5 subtype B Portuguese clades (26–79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998–2000) and 2000 (95% BCI, 1998–2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73–2.09) to 0.62 (95% BCI,.52–.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39–1.59) to 0.72 (95% BCI, .63–.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively. Conclusions The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
  • Loss of viral control in early HIV-1 infection is temporally associated with sequential escape from CD8(+) T cell responses and decrease in HIV-1-specific CD4(+) and CD8(+) T cell frequencies
    Item type: Journal Article
    Oxenius, Annette; Price, David A.; Trkola, Alexandra; et al. (2004)
    The Journal of Infectious Diseases
  • Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection
    Item type: Journal Article
    Carlisle, Louisa A.; Turk, Teja; Kusejko, Katharina; et al. (2019)
    The Journal of Infectious Diseases
    Background: Human immunodeficiency virus type 1 (HIV-1) genetic diversity increases over the course of infection and can be used to infer the time since infection and, consequently, infection recency, which are crucial for HIV-1 surveillance and the understanding of viral pathogenesis. Methods: We considered 313 HIV-infected individuals for whom reliable estimates of infection dates and next-generation sequencing (NGS)–derived nucleotide frequency data were available. Fractions of ambiguous nucleotides, obtained by population sequencing, were available for 207 samples. We assessed whether the average pairwise diversity calculated using NGS sequences provided a more exact prediction of the time since infection and classification of infection recency (<1 year after infection), compared with the fraction of ambiguous nucleotides. Results: NGS-derived average pairwise diversity classified an infection as recent with a sensitivity of 88% and a specificity of 85%. When considering only the 207 samples for which fractions of ambiguous nucleotides were available, the NGS-derived average pairwise diversity exhibited a higher sensitivity (90% vs 78%) and specificity (95% vs 67%) than the fraction of ambiguous nucleotides. Additionally, the average pairwise diversity could be used to estimate the time since infection with a mean absolute error of 0.84 years, compared with 1.03 years for the fraction of ambiguous nucleotides. Conclusions: Viral diversity based on NGS data is more precise than that based on population sequencing in its ability to predict infection recency and provides an estimated time since infection that has a mean absolute error of <1 year.
  • Effect of Immunosuppression on T-Helper 2 and B-Cell Responses to Influenza Vaccination
    Item type: Journal Article
    Egli, Adrian; Humar, Atul; Widmer, Lukas A.; et al. (2015)
    The Journal of Infectious Diseases
  • Untargeted Metabolite Profile Associations With Body Mass Index, Waist-Hip Ratio, and Antiretroviral Therapy in >1300 People With HIV: The Swiss HIV Cohort Study
    Item type: Journal Article
    Labarile, Marco; Schoepf, Isabella C.; Pasin, Chloé; et al. (2025)
    The Journal of Infectious Diseases
    Background How obesity and antiretroviral therapy (ART) are associated with specific metabolite profiles in people with HIV (PWH) is not well described. Methods In Swiss HIV Cohort Study participants, applying multiple linear regression, we analyzed untargeted metabolite profiles and their association with body mass index (BMI), waist–hip ratio (WHR), and current ART categorized based on the “third drug” plus individual ART drugs. Results We analyzed 1821 metabolites in 1302 PWH (median age 55 years, 78% male, 94% suppressed HIV RNA, median BMI 24.6 kg/m2, 46% overweight/obese). Ninety-four metabolites were associated with BMI, 66 with WHR, and 31 with either BMI or WHR and ART. 156, 173, and 60 metabolites were associated with non-nucleoside reverse transcriptase inhibitors, protease inhibitors, and integrase inhibitors, respectively. We identified specific patterns of metabolic perturbation for efavirenz, nevirapine, lopinavir, atazanavir, and elvitegravir. Most metabolites associated with tenofovir alafenamide were not associated with tenofovir disoproxil fumarate and vice versa. We found no evidence of any metabolite profiles associated with past zidovudine or stavudine exposure or any interactions between ART drug classes and BMI. Conclusions In PWH from Switzerland, untargeted metabolite profiling revealed multiple unreported associations with different ART agents, and previously reported associations with BMI.
  • The Oral Microbiome and All-Cause Mortality in a US Population-Representative Prospective Cohort
    Item type: Journal Article
    Vogtmann, Emily; Yano, Yukiko; Shi, Jianxin; et al. (2025)
    The Journal of Infectious Diseases
    No large studies have evaluated whether the human oral microbiome is directly associated with mortality. We evaluated prospective associations between the oral microbiome, measured using 16S ribosomal RNA gene sequencing, from participants aged 20-69 years in the 2009-2012 cycles of the National Health and Nutrition Examination Survey (NHANES) and all-cause mortality (N = 7721, representing similar to 194 million individuals). Alpha diversity was inversely associated with mortality, and some significant associations were observed with the beta diversity matrices. Higher relative abundances of Granulicatella and Lactobacillus were associated with increased risk, while Bacteroides was associated with decreased all-cause mortality at the genus level. Results suggest that oral bacterial communities may be important contributors to health and disease.
  • HIV-specific cellular immune response is inversely correlated with disease progression as defined by decline of CD4(+) T cells in relation to HIV RNA load
    Item type: Journal Article
    Oxenius, Annette; Price, David A.; Hersberger, Martin; et al. (2004)
    The Journal of Infectious Diseases
  • Association of Host Factors With Antibody Response to Seasonal Influenza Vaccination in Allogeneic Hematopoietic Stem Cell Transplant Patients
    Item type: Journal Article
    Linnik, Janina; Syedbasha, Mohameedyaseen; Kaltenbach, Hans-Michael; et al. (2022)
    The Journal of Infectious Diseases
    Background Influenza vaccination efficacy is reduced after hematopoietic stem cell transplantation (HSCT) and patient factors determining vaccination outcomes are still poorly understood. Methods We investigated the antibody response to seasonal influenza vaccination in 135 HSCT patients and 69 healthy volunteers (HVs) in a prospective observational multicenter cohort study. We identified patient factors associated with hemagglutination inhibition titers against A/California/2009/H1N1, A/Texas/2012/H3N2, and B/Massachusetts/2012 by multivariable regression on the observed titer levels and on seroconversion/seroprotection categories for comparison. Results Both regression approaches yielded consistent results but regression on titers estimated associations with higher precision. HSCT patients required 2 vaccine doses to achieve average responses comparable to a single dose in HVs. Prevaccination titers were positively associated with time after transplantation, confirming that HSCT patients can elicit potent antibody responses. However, an unrelated donor, absolute lymphocyte counts below the normal range, and treatment with calcineurin inhibitors lowered the odds of responding. Conclusions HSCT patients show a highly heterogeneous vaccine response but, overall, patients benefited from the booster shot and can acquire seroprotective antibodies over the years after transplantation. Several common patient factors lower the odds of responding, urging identification of additional preventive strategies in the poorly responding groups. Clinical Trials Registration NCT03467074.
  • The Bacterial Stress-Responsive Hsp90 Chaperone (HtpG) Is Required for the Production of the Genotoxin Colibactin and the Siderophore Yersiniabactin in Escherichia coli
    Item type: Journal Article
    Garcie, Christophe; Tronnet, Sophie; Garénaux, Amélie; et al. (2016)
    The Journal of Infectious Diseases
    The genotoxin colibactin, synthesized by Escherichia coli, is a secondary metabolite belonging to the chemical family of hybrid polyketide/nonribosomal peptide compounds. It is produced by a complex biosynthetic assembly line encoded by the pks pathogenicity island. The presence of this large cluster of genes in the E. coli genome is invariably associated with the high-pathogenicity island, encoding the siderophore yersiniabactin, which belongs to the same chemical family as colibactin. The E. coli heat shock protein HtpG (Hsp90Ec) is the bacterial homolog of the eukaryotic molecular chaperone Hsp90, which is involved in the protection of cellular proteins against a variety of environmental stresses. In contrast to eukaryotic Hsp90, the functions and client proteins of Hsp90Ec are poorly known. Here, we demonstrated that production of colibactin and yersiniabactin is abolished in the absence of Hsp90Ec. We further characterized an interplay between the Hsp90Ec molecular chaperone and the ClpQ protease involved in colibactin and yersiniabactin synthesis. Finally, we demonstrated that Hsp90Ec is required for the full in vivo virulence of extraintestinal pathogenic E. coli. This is the first report highlighting the role of heat shock protein Hps90Ec in the production of two secondary metabolites involved in E. coli virulence.
  • Identification of Epstein‐Barr Virus (EBV)–Infected Lymphocyte Subtypes by Flow Cytometric In Situ Hybridization in EBV‐Associated Lymphoproliferative Diseases
    Item type: Journal Article
    Kimura, Hiroshi; Miyake, Kanae; Yamauchi, Yohei; et al. (2009)
    The Journal of Infectious Diseases
    To diagnose Epstein-Barr virus (EBV)–associated diseases and to explore the pathogenesis of EBV infection, not only must the EBV load be measured, but EBV-infected cells must also be identified. We established a novel flow cytometric in situ hybridization assay to detect EBV⁺ suspension cells using a peptide nucleic acid probe specific for EBV-encoded small RNA (EBER). By enhancing fluorescence and photostability, we successfully stained EBER and surface antigens on the same cells. In 3 patients with hydroa vacciniforme–like lymphoproliferative disease, we demonstrated that 1.7%–25.9% of peripheral lymphocytes were infected with EBV and specifically identified these lymphocytes as CD3⁺CD4⁻CD8⁻ γδ T cell receptor–positive T cells. The results indicate that this novel and noninvasive assay is a direct and reliable method of characterizing EBV-infected lymphocytes that can be used not only to diagnose EBV infection but also to clarify the pathogenesis of EBV-associated diseases.
Publications 1 - 10 of 17