Journal of Infectious Diseases

BACKGROUND: Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and an increasingly frequent cause of opportunistic infections. Mycobacterium abscessus complex (MAB) is one of the major NTM lung pathogens which disproportionately colonize and infect the lungs of individuals with cystic fibrosis (CF). MAB infection can persist for years, and antimicrobial treatment is frequently ineffective. METHODS: We sequence the genomes of 175 isolates longitudinally collected from 30 patients with MAB lung infection...

BACKGROUND: Despite intensive prophylactic and pre-emptive measures, infections remain an important cause of morbidity and mortality in pediatric recipients of allogeneic hematopoietic cell transplantation (allo-HCT). Disruption of the gut microbiota has been linked to clinical outcomes after adult allo-HCT. This study evaluated whether these or differing microbiota disruptions or signatures were associated with risk of infection in pediatric allo-HCT. METHODS: In a prospective observational study, fecal samples from 74 children were collected prior to conditioning and at the time of neutrophil recovery and profiled by means of 16S ribosomal rRNA sequencing...

INTRODUCTION: Previous studies reported inconsistent findings regarding the association between respiratory syncytial virus (RSV) subgroup distribution and timing of RSV seasonal epidemics, possibly due to not accounting for confounders such as meteorological factors. We aimed to improve the understanding of the association through a global-level systematic analysis that accounted for these potential confounders. METHODS: We compiled published data on RSV seasonality through a systematic literature review, and supplemented with unpublished data shared by international collaborators...

BACKGROUND: Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections in adults that can result in hospitalisations. Estimating RSV-associated hospitalisation is critical for planning RSV-related healthcare across Europe. METHODS: We gathered RSV-associated hospitalisation estimates from the RSV Consortium in Europe (RESCEU) for adults in Denmark, England, Finland, Norway, Netherlands, and Scotland from 2006-2017. We extrapolated these estimates to 28 EU countries using nearest-neighbour matching, multiple imputations, and two sets of 10 indicators...

BACKGROUND: No overall estimate of RSV-associated hospitalisations in children under 5 years has been published for the European Union (EU). We aimed to estimate the RSV hospitalisation burden in children under 5 years in EU countries and Norway, by age group. METHODS: We collated national RSV-associated hospitalisation estimates calculated using linear regression models via the RESCEU project for Denmark, England, Finland, Norway, the Netherlands and Scotland during 2006-2018...

BACKGROUND: Pulmonary tuberculosis (TB) and lung cancer (LC) have similar clinical symptoms and atypical imaging findings which are easily misdiagnosed. There is an urgent need for a noninvasive and accurate biomarker to distinguish LC from TB. METHODS: A total of 694 subjects were enrolled and divided into discovery set (n = 122), identification set (n = 214), and validation set (n = 358). Metabolites were identified by multivariate and univariate analyses...

BACKGROUND: Immunity to Streptococcus pyogenes in high burden settings is poorly understood. We explored S. pyogenes nasopharyngeal colonization after intranasal live attenuated influenza vaccine (LAIV) among Gambian children aged 24-59 months, and resulting serological response to 7 antigens. METHODS: A post-hoc analysis was performed in 320 children randomized to receive LAIV at baseline (LAIV group) or not (control). S. pyogenes colonization was determined by quantitative Polymerase Chain Reaction (qPCR) on nasopharyngeal swabs from baseline (D0), day 7 (D7) and day 21 (D21)...

Mass drug administration programs targeting filarial infections depend on diagnostic tools that are sensitive and specific. The co-endemicity of Loa loa with other filarial species often hampers the control programs. LL2634 was identified as the most promising target among several highly repeated targets, with sensitivity between 500 ag and 1 fg of genomic DNA. Using DNA from infected individuals, LL2643 qPCR was positive in all individuals. LL2643 was detected in plasma derived circulating cell-free DNA (ccfDNA) from 48 of 53 mf positive patients...

BACKGROUND: This study examined the effects of HIV on resting state functional connectivity (RSFC) in a large cohort of people living with HIV (PWH) and healthy controls without HIV (PWoH). Within PWH analyses focused on the effects of viral suppression and cognitive impairment on RSFC. METHODS: A total of 316 PWH on stable combination antiretroviral therapy and 209 demographically matched PWoH were scanned at a single institution. Effects of the virus were examined by grouping PWH by detectable (viral load > 20 copies/ml; VLD) and undetectable (VLU) viral loads and as being cognitively impaired (CI) (Global Deficit Score ≥ 0...

BACKGROUND: Bone mineral density (BMD) loss may be accelerated in people with HIV (PLWH). It is unknown whether an individual polygenic risk score (PRS) is associated with low BMD in PLWH. METHODS: We included Swiss HIV Cohort Study participants of self-reported European descent, each with >2 per-protocol Dual X-ray Absorptiometry (DXA) measurements >2 years apart (2011-2020). We obtained uni-/multivariable odds ratios (OR) for DXA-defined osteoporosis based on traditional and HIV-related osteoporosis risk factors and a genome-wide PRS built from 9413 single nucleotide polymorphisms associated with low BMD in the general population...

BACKGROUND: On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the two different lineages present in the 2021 and 2022 outbreaks revealed the presence of G->A mutations occurring in the 5'GpA context, indicative of APOBEC3 cytidine deaminase activity. METHODS: By using a sensitive PCR (3D-PCR) method allowing differential amplification of AT-rich DNA, we analyzed the level of APOBEC3-induced MPXV editing in infected cells and in patients...

BACKGROUND: Herpes simplex virus-1 (HSV-1) can cause severe infections in immunocompromised individuals. In these patients, emergence of drug-resistance mutations causes difficulties in the infection management. METHODS: Seventeen HSV-1 isolates were obtained from orofacial and anogenital lesions in a leaky severe combined immunodeficiency (SCID) patient over 7-years' time before and after stem cell transplantation. Spatial and temporal evolution of drug-resistance was characterized genotypically [Sanger sequencing and next-generation sequencing (NGS) of viral thymidine kinase (TK) and DNA polymerase (DP)], and phenotypically...

The anti-spike (S), anti-nucleocapsid (N), and neutralizing activities of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of pooled plasma derived from donors in Japan from January 2021 to April 2022 were evaluated. Anti-S titers and neutralizing activities showed a wave-like trend affected by daily vaccinations and/or the number of reported cases of SARS-CoV-2 infections, whereas anti-N titers remained at negative levels. These results suggest that anti-S and neutralizing titers would fluctuate in pooled plasma in future...

BACKGROUND: Despite scale-up of seasonal malaria chemoprevention (SMC) with sulfadoxine-pyrimethamine and amodiaquine (SP-AQ) in children <5 years old in Burkina Faso, malaria incidence remains high, raising concerns regarding SMC effectiveness and selection of drug resistance. Using a case-control design, we determined associations between SMC drug levels, drug resistance markers, and presentation with malaria. METHODS: We enrolled 310 children presenting at health facilities in Bobo-Dioulasso...

Mycobacterium ulcerans causes Buruli ulcer, the third most frequent mycobacterial disease after tuberculosis and leprosy. Transient clinical deteriorations, known as paradoxical reactions, occur in some patients during or after antibiotic treatment. We investigated the clinical and biological features of PRs in a prospective cohort of BU patients from Benin including forty-one patients. Neutrophil counts decreased from baseline to day 90 and IL-6, G-CSF and VEGF were the cytokines displaying a significant monthly decrease relative to baseline...

BACKGROUND: Face masks have been critical in the COVID-19 pandemic, but supplies were sometimes limited and disposable masks contribute greatly to environmental waste. Studies suggest that filtration capacity is retained with repeated use, and surveys indicate many people re-use surgical masks. However, the impact of mask re-use on the host is under-studied. METHODS: We applied 16S rRNA gene sequencing to investigate the bacterial microbiome of the facial skin and oropharynx of individuals randomized to wearing fresh surgical masks daily versus masks re-used for one week...

BACKGROUND: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health challenge. Limitations to AMR surveillance reporting, alongside reduction in culture-based susceptibility testing, has resulted in a need for rapid diagnostics and strain detection. We investigated Nanopore sequencing time, and depth, to accurately identify closely related N. gonorrhoeae isolates, compared to Illumina sequencing. METHODS: N. gonorrhoeae strains collected from a London Sexual Health clinic were cultured and sequenced with MiSeq and MinION sequencing platforms...

BACKGROUND: NVX-CoV2373 is an efficacious COVID-19 vaccine comprising full-length 5-µg recombinant SARS-CoV-2 spike (rS) glycoprotein and Matrix-M™ adjuvant. Phase 2 of a randomized, placebo-controlled, phase 1/2 trial in healthy adults (18-84 years) previously reported good safety/tolerability and robust humoral immunogenicity. METHODS: Participants were randomized to placebo or 1 or 2 doses of 5-µg or 25-µg rS with 50 µg Matrix-M adjuvant 21 days apart...

BACKGROUND: Klebsiella pneumoniae liver abscess (KPLA) with extrahepatic migratory infections is defined as invasive KPLA (IKPLA). The type VI secretion system (T6SS) is involved in the pathogenesis of KPLA. We hypothesized that T6SS play a role in the IKPLA. METHODS: 16S rRNA gene sequencing was performed on abscess samples. Polymerase chain reaction (PCR) and reverse transcription (RT)-PCR was used to validate the expression difference of T6SS hallmark genes. In vitro and in vivo experiments were performed to identify the pathogenic feature of T6SS...

BACKGROUND: Women's increased risk of HIV acquisition during pregnancy and postpartum may be mediated by changes in vaginal microbiota and/or cytokines. METHODS: A cohort of 80 HIV-1-seronegative Kenyan women contributed 409 vaginal samples at six pregnancy timepoints: periconception, positive pregnancy test, first trimester, second trimester, third trimester, and postpartum. Concentrations of vaginal bacteria linked with HIV risk and Lactobacillus species were measured using quantitative polymerase chain reaction...