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

Suivi rétrospectif des infections systémiques à adénovirus, après allogreffe de cellules souches hématopoïétiques (intérêt de la PCR en temps réel)

PARIS-BIUP (751062107) / SudocSudocFranceF

Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform

Genotypic testing is often recommended to improve the management of patients infected with human immunodeficiency virus (HIV). To help combat this major pandemic, next-generation sequencing (NGS) techniques are widely used to analyse resistance to antiretroviral drugs. In this study, we used a Vela Sentosa kit (Vela Diagnostics, Kendall, Singapore), which is usually used for the Ion Torrent personal genome machine (PGM) platform, to sequence HIV using the Illumina Miseq platform. After RNA extraction and reverse transcriptase-polymerase chain reaction (RT-PCR), minor modifications were applied to the Vela Sentosa kit to adapt it to the Illumina Miseq platform. Analysis of the results showed the same mutations present in the samples using both sequencing platforms. The total number of reads varied from 185,069 to 752,343 and from 642,162 to 2,074,028 in the Ion Torrent PGM platform and the Illumina Miseq platform, respectively. The average depth was 21,955 and 46,856 for Ion Torrent PGM and Illumina Miseq platforms, respectively. The cost of sequencing a run of eight samples was quite similar between the two platforms (about USD 1790 for Illumina Miseq and about USD 1833 for Ion Torrent PGM platform). We have shown for the first time that it is possible to adapt and use the Vela Sentosa kit for the Illumina Miseq platform to obtain high-quality results with a similar cost

Postextubation Stridor in Severe COVID-19

International audienceBACKGROUND: During the coronavirus disease 2019 (COVID-19) pandemic, 60-80% of patients admitted to ICU require mechanical ventilation for respiratory distress. We aimed to compare the frequency of postextubation stridor (PES) and to explore risk factors in COVID-19 subjects compared to those without COVID-19. METHODS: We performed an observational retrospective study on subjects admitted for severe COVID-19 requiring mechanical ventilation > 48 h during the first and second waves in 2020 and compared these subjects to historical controls without COVID-19 who received mechanical ventilation > 48 h between 2016-2019. The primary outcome was the frequency of PES, defined as audible stridor within 2 h following extubation. RESULTS: Of the 134 subjects admitted with severe COVID-19 requiring mechanical ventilation, 96 were extubated and included and compared to 211 controls. The frequency of PES was 22.9% in the COVID-19 subjects and 3.8% in the controls (P < .001). Factors independently associated with PES were having COVID-19 (odds ratio 3.72, [95% CI 1.24-12.14], P = .02), female sex (odds ratio 5.77 [95% CI 2.30-15.64], P < .001), and tube mobilization or re-intubation or prone positioning (odds ratio 3.01 [95% CI 1.04-9.44], P = .047) after adjustment on Simplified Acute Physiology Score II expanded). During the first wave, PES was significantly more common in subjects with a positive SARS-CoV-2 RT-PCR test on tracheal samples on the day of extubation (73.3% vs 24.3%, P = .018). CONCLUSIONS: PES affected nearly one-quarter of subjects with COVID-19, a proportion significantly higher than that seen in controls. Independent risk factors for PES were COVID-19, female sex, and tube mobilization or re-intubation or prone positioning. PES was associated with persistent viral shedding at the time of extubation. Copyrigh

Invasive Aspergillosis associated with Covid-19: A word of caution

International audienceIntroduction: Invasive pulmonary aspergillosis is a well-known complication of acute respiratory distress syndrome, the most serious manifestation of COVID-19. Four recent studies have reported its incidence among ICU COVID-19 patients. However, they do not share the same case definition, and have provided conflicting results. In this paper we have aimed at reported the incidence of invasive pulmonary aspergillosis for COVID-19 patients in our ICU, and at comparing the different definitions in order to assess their respective relevance. Methods: Retrospective cohort study of critically ill patients with severe COVID-19 requiring ICU management between 1st March and 30th April 2020. Results: Our results showed significantly lower incidence of invasive pulmonary aspergillosis (1.8%;1/53), compared to three out of four previous studies, and wide variation in the numbers of cases with regard to the different definitions. Conclusion: Large-scale studies are needed for a better definition and a more accurate estimation of invasive pulmonary aspergillosis coinfection during COVID-19

Enterovirus infections in hospitals of Ile de France region over 2013.

International audienceThe monitoring and genotyping of Enterovirus (EV) infections can help to associate particular or severe clinical manifestations with specific EV types and to identify the aetiology of infectious outbreaks. To describe the epidemiological features of EV infections diagnosed during the year 2013 in the Greater Paris area (Ile de France). During 2013, 2497 samples taken from 470 patients in 33 hospitals of Ile-de France were tested for EV genome by RT-PCR. EV genotyping was performed by the National Reference Centre (NRC) laboratories. EV infections were retrospectively reviewed by retrieving clinical and genotyping data from the NRC database. Of the 2497 samples, 490 (19.6%) was positive for EV genome detection. These EV infections represented 88.7% and 24.1%, respectively, of all reported regional and national infections. Twenty-seven different genotypes were identified. Echovirus 30 (E-30) accounted for 54.1% of all characterized strains and caused a large outbreak. Four severe neonatal infections were reported, of which two were caused by EV-A71. Respiratory infections involving EV-D68 were observed in two adults. One fatal case of Coxsackievirus A2-associated myocarditis was reported. Monitoring EV infections in combination with EV genotyping via the French EV network characterized the epidemiology of EV infections in the Ile de France region in 2013 and documented severe EV infections associated with EV-A71 or CV-A2

New Introductions of Enterovirus 71 Subgenogroup C4 Strains, France, 2012

In France during 2012, human enterovirus 71 (EV-A71) subgenogroup C4 strains were detected in 4 children hospitalized for neonatal fever or meningitis. Phylogenetic analysis showed novel and independent EV-A71 introductions, presumably from China, and suggested circulation of C4 strains throughout France. This observation emphasizes the need for monitoring EV-A71 infections in Europe

Association of ventilator type with hospital mortality in critically ill patients with SARS-CoV2 infection:a prospective study

BACKGROUND: To evaluate the association between ventilator type and hospital mortality in patients with acute respiratory distress syndrome (ARDS) related to COVID-19 (SARS-CoV2 infection), a single-center prospective observational study in France. RESULTS: We prospectively included consecutive adults admitted to the intensive care unit (ICU) of a university-affiliated tertiary hospital for ARDS related to proven COVID-19, between March 2020 and July 2021. All patients were intubated. We compared two patient groups defined by whether an ICU ventilator or a less sophisticated ventilator such as a sophisticated turbine-based transport ventilator was used. Kaplan–Meier survival curves were plotted. Cox multivariate regression was performed to identify associations between patient characteristics and hospital mortality. We included 189 patients (140 [74.1%] men) with a median age of 65 years [IQR, 55–73], of whom 61 (32.3%) died before hospital discharge. By multivariate analysis, factors associated with in-hospital mortality were age ≥ 70 years (HR, 2.11; 95% CI, 1.24–3.59; P = 0.006), immunodeficiency (HR, 2.43; 95% CI, 1.16–5.09; P = 0.02) and serum creatinine ≥ 100 µmol/L (HR, 3.01; 95% CI, 1.77–5.10; P < 0.001) but not ventilator type. As compared to conventional ICU (equipped with ICU and anesthesiology ventilators), management in transient ICU (equipped with non-ICU turbine-based ventilators) was associated neither with a longer duration of invasive mechanical ventilation (18 [IQR, 11–32] vs. 21 [13–37] days, respectively; P = 0.39) nor with a longer ICU stay (24 [IQR, 14–40] vs. 27 [15–44] days, respectively; P = 0.44). CONCLUSIONS: In ventilated patients with ARDS due to COVID-19, management in transient ICU equipped with non-ICU sophisticated turbine-based ventilators was not associated with worse outcomes compared to standard ICU, equipped with ICU ventilators. Although our study design is not powered to demonstrate any difference in outcome, our results after adjustment do not suggest any signal of harm when using these transport type ventilators as an alternative to ICU ventilators during COVID-19 surge. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13613-022-00981-2

Unchanged Characteristics and Survival among Critically Ill COVID-19 Patients during First, Second, and Third Waves: A Prospective Observational Cohort

International audienceBackground: This study was carried out to compare characteristics and outcomes in patients with acute respiratory failure related to COVID-19 during first, second, and third waves. Methods: We included consecutive adults admitted to the intensive care unit between March 2020 and July 2021. We compared three groups defined by the epidemic intake phase: waves 1 (W1), 2 (W2), and 3 (W3). Results: We included 289 patients. Two hundred and eight (72%) patients were men with a median age of 63 years (IQR: 54-72), of whom 68 (23.6%) died in hospital. High-flow nasal oxygen (HFNO) was inversely associated with the need for invasive mechanical ventilation (MV) in multivariate analysis (p = 0.003) but not dexamethasone (p = 0.25). The day-90 mortality rate did not vary from W1 (27.4%) to W2 (23.9%) and W3 (22%), p = 0.67. By multivariate analysis, older age (odds ratio [OR]: 0.94/year, p < 0.001), immunodeficiency (OR: 0.33, p = 0.04), acute kidney injury (OR: 0.26, p < 0.001), and invasive MV (OR: 0.13, p < 0.001) were inversely associated with higher day-90 survival as opposed to the use of intermediate heparin thromboprophylaxis dose (OR: 3.21, p = 0.006). HFNO use and dexamethasone were not associated with higher day-90 survival (p = 0.24 and p = 0.56, respectively). Conclusions: In patients with acute respiratory failure due to COVID-19, survival did not change between first, second, and third waves while the use of invasive MV decreased. HFNO or intravenous steroids were not associated with better outcomes, whereas the use of intermediate dose of heparin for thromboprophylaxis was associated with higher day-90 survival. Larger multicentric studies are needed to confirm our findings

Multirecombinant Enterovirus A71 Subgenogroup C1 Isolates Associated with Neurologic Disease, France, 2016–2017

International audienceIn 2016, an upsurge of neurologic disease associated with infection with multirecombinant enterovirus A71 subgenogroup C1 lineage viruses was reported in France. These viruses emerged in the 2000s; 1 recombinant is widespread. This virus lineage has the potential to be associated with a long-term risk for severe disease among children