Antiretroviral-naive and -treated HIV-1 patients can harbour more resistant viruses in CSF than in plasma

Objectives The neurological disorders in HIV-1-infected patients remain prevalent. The HIV-1 resistance in plasma and CSF was compared in patients with neurological disorders in a multicentre study. Methods Blood and CSF samples were collected at time of neurological disorders for 244 patients. The viral loads were >50 copies/mL in both compartments and bulk genotypic tests were realized. Results On 244 patients, 89 and 155 were antiretroviral (ARV) naive and ARV treated, respectively. In ARV-naive patients, detection of mutations in CSF and not in plasma were reported for the reverse transcriptase (RT) gene in 2/89 patients (2.2%) and for the protease gene in 1/89 patients (1.1%). In ARV-treated patients, 19/152 (12.5%) patients had HIV-1 mutations only in the CSF for the RT gene and 30/151 (19.8%) for the protease gene. Two mutations appeared statistically more prevalent in the CSF than in plasma: M41L (P = 0.0455) and T215Y (P = 0.0455). Conclusions In most cases, resistance mutations were present and similar in both studied compartments. However, in 3.4% of ARV-naive and 8.8% of ARV-treated patients, the virus was more resistant in CSF than in plasma. These results support the need for genotypic resistance testing when lumbar puncture is performe

Autoantibodies against type I IFNs in patients with critical influenza pneumonia

In an international cohort of 279 patients with hypoxemic influenza pneumonia, we identified 13 patients (4.6%) with autoantibodies neutralizing IFN-alpha and/or -omega, which were previously reported to underlie 15% cases of life-threatening COVID-19 pneumonia and one third of severe adverse reactions to live-attenuated yellow fever vaccine. Autoantibodies neutralizing type I interferons (IFNs) can underlie critical COVID-19 pneumonia and yellow fever vaccine disease. We report here on 13 patients harboring autoantibodies neutralizing IFN-alpha 2 alone (five patients) or with IFN-omega (eight patients) from a cohort of 279 patients (4.7%) aged 6-73 yr with critical influenza pneumonia. Nine and four patients had antibodies neutralizing high and low concentrations, respectively, of IFN-alpha 2, and six and two patients had antibodies neutralizing high and low concentrations, respectively, of IFN-omega. The patients' autoantibodies increased influenza A virus replication in both A549 cells and reconstituted human airway epithelia. The prevalence of these antibodies was significantly higher than that in the general population for patients 70 yr of age (3.1 vs. 4.4%, P = 0.68). The risk of critical influenza was highest in patients with antibodies neutralizing high concentrations of both IFN-alpha 2 and IFN-omega (OR = 11.7, P = 1.3 x 10(-5)), especially those <70 yr old (OR = 139.9, P = 3.1 x 10(-10)). We also identified 10 patients in additional influenza patient cohorts. Autoantibodies neutralizing type I IFNs account for similar to 5% of cases of life-threatening influenza pneumonia in patients <70 yr old

Exploration of the urinary tract bacterial microbiota by culturomics and metagenomic methods

L’urine a longtemps été considérée stérile.Ce travail visait à établir le répertoire des bactéries connues dans les voies urinaires humaines par une revue de la littérature et à implémenter ce répertoire en analysant des échantillons d’urine par culturomics et métagénomique. 562 espèces bactériennes ont été décrites dans des échantillons d’urine humains dans la littérature. 62,6% ont été associées à un cas d'infection humaine. Parmi les 441 échantillons d’urine analysés par culturomics, 459 espèces bactériennes différentes ont été isolées, dont 264 jamais décrites dans l'urine, 18 nouvelles espèces. Parmi les 684 espèces bactériennes isolées au moins une fois en culture à partir d’échantillons d'urine, 424 (62%) avaient déjà été isolées du microbiote intestinal. Parmi les espèces retrouvées uniquement en métagénomique figurent des bactéries extrêmophiles. Il existe un microbiote des voies urinaires humaines qui peut être décrit par culturomics et métagénomique.Urine was usually considered sterile. This work aimed to establish the repertoire of known bacteria in the human urinary tract through a review of the literature and to implement this repertoire by analyzing urine samples by culturomics and metagenomics.In literature, 562 bacterial species have been described in human urine samples, in which 62.6% were associated with one case of human infection.Of the 441 urine samples analyzed by culturomics, 459 different bacterial species were isolated, of which 264 never described in the urine, 18 new species.Of the 684 bacterial species isolated at least once in culture from urine samples, 424 (62%) had already been isolated from the gut microbiota.Extremophilic bacteria and archaea are identified among the species found only with metagenomics method.There is a microbiota of the human urinary tract that can be described by culturomics and metagenomics