Respiratory syncytial virus vs. Influenza virus infection: mortality and morbidity comparison over 7 epidemic seasons in an elderly population

BACKGROUND

Respiratory syncytial virus (RSV) infection is gaining interest due to the recent development of vaccines, but it is still misdiagnosed in the elderly. The primary objective was to compare all-cause mortality at day 30. Secondary objectives were to compare clinical presentation, and rates of consolidative pneumonia, hospitalization, and intensive care unit (ICU) admission.

METHODS

Single-centre retrospective study conducted in a French university hospital during 7 epidemic seasons. All patients aged ≥75 years were included.

RESULTS

558 patients were included: 125 with RSV and 433 with Influenza. Median age was 84.8 years. RSV patients had more respiratory symptoms (wheezing, dyspnea), whereas Influenza patients had more general symptoms (fever, asthenia, myalgia). Consolidative pneumonia (28.8% vs. 17.2%; p = 0.004), hospitalization rates (83.2% vs. 70%; p = 0.003), ICU admissions (7.2% vs. 3.0%; p = 0.034) and length of stay (9 days [2-16] vs. 5 days [0-12]; p = 0.002), were higher in the RSV group. Mortality rates at day 30 were comparable (RSV 9.6%, Influenza 9.7%; p = 0.973).

CONCLUSIONS

This study included the largest cohort of RSV-infected patients aged over 75, documented in-depth thus far. RSV shares a comparable mortality rate with Influenza but is associated with higher rates of consolidative pneumonia, hospitalization, ICU admissions, and extended hospital stays.

Beyond the First Year: Epidemiology and Management of Late-Onset Opportunistic Infections After Kidney Transplantation

Late opportunistic infections (OI) occurring beyond the first year after kidney transplantation (KT) are poorly described and not targeted by prophylactic strategies. We performed a ten-year retrospective monocentric cohort study describing epidemiology, risk factors and impact of late OI occurring 1 year after KT. We included clinically symptomatic OI requiring treatment besides BK virus nephropathy. Control groups included early OI occurring in the first year after KT, and KT recipients without OI since KT and alive with a functional allograft at 1 year. Among 1066 KT recipients, 185 (19.4%) presented a first episode of OI 21.0 (8.0-45.0) months after KT: 120 late OI (64.9%) and 65 early OI (35.1%). Late OI were mainly viral (N = 83, 69.2%), mostly herpes zoster (HZ) (N = 36, 43.4%). Pneumocystis represented most late fungal infections (N = 12/25, 48%). Compared to early OI, we reported more pneumocystis (p = 0.002) and less invasive aspergillosis (p = 0.01) among late OI. Patients with late OI were significatively younger at KT (54.0 ± 13.3 vs. 60.2 ± 14.3 years, p = 0.05). Patient and allograft survival rates between late OI and control groups were similar. Only age was independently associated with mortality. While late OI were not associated with higher mortality or graft loss, implementing prophylactic strategies might prevent such infections.

Retrospective study on the association of human herpesvirus reactivation with severe DRESS: A description of blood and skin reactivations

BACKGROUND

Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS) is a severe adverse event (mortality of 10%). Its pathophysiology involves herpesviruses, particularly HHV-6, but the exact mechanisms are still poorly understood.

OBJECTIVE

To describe severe cases of DRESS and especially their association with herpesvirus reactivation.

METHODS

This study was a multicentre case series conducted between 2007 and 2021 at five University Hospital Centres in France. The study included patients who had severe DRESS, which was defined as death, transfer to the intensive care unit (ICU), or severe damage to internal organs. We excluded patients without blood PCR sample, without a drug formally attributed or with RegiSCAR score < 6. We collected data on severity, causative drug, associated visceral damage and results of viral blood PCRs. HHV-6 reactivation was studied in skin biopsies by detection of small non-coding transcripts (HHV-6 miR-aU14) and a late viral protein (GP82/105).

RESULTS

Fifty-two patients were included (29 female, median age 62, interquartile range (IQR) [37;72]). Eight patients (15%) died, 13 (27%) were admitted to ICU. Most patients (n = 34; 65%) had multisystem involvement: most frequent was liver (n = 46; 88%), then renal failure (n = 24; 46%). Forty patients (77%) had at least one blood viral reactivation among HHV-6, EBV or CMV, of which 21 (53%) had at least two. Median time of blood HHV-6 reactivation was 24 days (IQR [20;35]). HHV-6 reactivation was demonstrated in 15 out of 20 skin biopsies, with a median time of 11 days [9;17].

CONCLUSIONS

We confirmed the high rate of HHV-6 reactivation in severe DRESS and demonstrated cutaneous HHV-6 reactivation using small non-coding transcripts (HHV-6 miR-aU14), which preceded viral PCR positivity in blood. These results suggest that HHV-6 reactivation during DRESS may start in skin. Furthermore, search for miR-aU14 in skin biopsy could become a useful diagnostic tool for early detection of HHV-6 reactivation.

High unrecognized SARS-CoV-2 exposure of newly admitted and hospitalized psychiatric patients

BACKGROUND

Patients with pre-existing mental disorders are at higher risk for SARS-CoV-2 infection and adverse outcomes, and severe mental illness, including mood and psychosis spectrum disorders, is associated with increased mortality risk. Despite their increased risk profile, patients with severe mental illness have been understudied during the pandemic, with limited estimates of exposure in inpatient settings.

OBJECTIVE

The aim of this study was to describe the SARS-CoV-2 seroprevalence and antibody titers, and pro-inflammatory cytokine concentrations of newly admitted or hospitalized psychiatric inpatients without known history of COVID-19 infection, using robust quantitative multi-antigen assessments, and compare patients' exposure to that of hospital staff.

METHODS

This multi-centric, cross-sectional study compared SARS-CoV-2 seroprevalence and titers of 285 patients (University Psychiatric Centre Duffel [UPCD] N = 194; Assistance-Publique-Hopitaux de Paris [AP-HP] N = 91), and 192 hospital caregivers (UPCD N = 130; AP-HP N = 62) at two large psychiatric care facilities between January 1st and the May 30th 2021. Serum levels of SARS-CoV-2 antibodies against Spike proteins (full length), spike subunit 1 (S1), spike subunit 2 (S2), spike subunit 1 receptor binding domain (S1-RBD) and Nucleocapsid proteins were quantitatively determined using an advanced capillary Western Blot technique. To assess the robustness of the between-group seroprevalence differences, we performed sensitivity analyses with stringent cut-offs for seropositivity. We also assessed peripheral concentrations of IL-6, IL-8 and TNF-a using ELLA assays. Secondary analyses included comparisons of SARS-CoV-2 seroprevalence and titers between patient diagnostic subgroups, and between newly admitted (hospitalization ≤ 7 days) and hospitalized patients (hospitalization > 7 days) and correlations between serological and cytokines.

RESULTS

Patients had a significantly higher SARS-CoV-2 seroprevalence (67.85 % [95% CI 62.20-73.02]) than hospital caregivers (27.08% [95% CI 21.29-33.77]), and had significantly higher global SARS-CoV-2 titers (F = 29.40, df = 2, p < 0.0001). Moreover, patients had a 2.51-fold (95% CI 1.95-3.20) higher SARS-CoV-2 exposure risk compared to hospital caregivers (Fisher's exact test, P < 0.0001). No difference was found in SARS-CoV-2 seroprevalence and titers between patient subgroups. Patients could be differentiated most accurately from hospital caregivers by their higher Spike protein titers (OR 136.54 [95% CI 43.08-481.98], P < 0.0001), lower S1 (OR 0.06 [95% CI 0.02-0.15], P < 0.0001) titers and higher IL-6 (OR 3.41 [95% CI 1.73-7.24], P < 0.0001) and TNF-α (OR 34.29 [95% CI 5.00-258.87], P < 0.0001) and lower titers of IL-8 (OR 0.13 [95% CI 0.05-0.30], P < 0.0001). Seropositive patients had significantly higher SARS-COV-2 antibody titers compared to seropositive hospital caregivers (F = 19.53, df = 2, P < 0.0001), while titers were not different in seronegative individuals. Pro-inflammatory cytokine concentrations were not associated with serological status.

CONCLUSION

Our work demonstrated a very high unrecognized exposure to SARS-CoV-2 among newly admitted and hospitalized psychiatric inpatients, which is cause for concern in the context of highly robust evidence of adverse outcomes following COVID-19 in psychiatric patients. Attention should be directed toward monitoring and mitigating exposure to infectious agents within psychiatric hospitals.

Le déficit en interféron de type I n’altère pas la réponse lymphocytaire B mémoire contre le SARS-CoV-2 après vaccination par ARNm

Introduction

Les vaccins à ARN messagers ont joué un rôle majeur dans la lutte contre la pandémie de SARS-CoV-2 grâce à une excellente efficacité et sécurité clinique. Ces vaccins ont été développés suite à des années de recherche fondamentale, dont l’une des étapes cruciales a été de remplacer l’uridine de l’ARNm par de la 1-méthyl-pseudo-uridine afin d’éviter la reconnaissance par les récepteurs de l’immunité innée, notamment le toll-like-receptor (TLR) 7. Une hypothèse, très fréquemment défendue mais jamais étayée expérimentalement, est que cet ARN modifié garde une activité immunostimulatrice à bas bruit permettant la production d’interféron de type I, agissant comme un adjuvant du vaccin. Les interférons de type I sont des cytokines antivirales essentielles et les patients ayant un déficit dans les voies de l’interféron de type I sont à haut risque de COVID-19 sévère. Dans ce travail, nous avons analysé la réponse lymphocytaire B au vaccin à ARNm de patients présentant l’absence de signalisation par les interférons de type I. Ceci nous a permis de savoir si les vaccins par ARNm permettaient d’établir une réponse lymphocytaire B robuste en l’absence d’interféron de type I.

Patients et méthodes

Nous avons constitué trois cohortes de patients (i) des patients avec des déficits génétiques sur les voies de l’interféron de type I : 2 patients avec une mutation homozygote d’IRF7 (facteur de transcription responsable de la production d’interférons de Type I, notamment en aval de TLR7) et un patient avec une déficit hémizygote de TLR7 (ii) des patients ayant des auto-anticorps neutralisant les interférons alpha et oméga, dans le cadre d’une polyendocrinopathie auto-immune de type I (APS-1, n = 14) (iii) des patients ayant des auto-anticorps neutralisant les interféron, associés à l’âge, une entité récemment décrite et particulièrement fréquente chez les sujets âgés (n = 8). Ces sujets ont été comparés à 29 contrôles sains. Tous étaient naïfs du COVID-19 et ont reçu 2 doses de vaccin à ARNm (BNT162n2 ou mRNA1273). Les patients ont été prélevés à différents point de temps, dans les 3 premiers mois et entre 3 et 7 mois après la seconde dose. La réponse sérologique a été évaluée par ELISA anti-IgG et IgA RBD (receptor binding domain de la Spike) et la neutralisation sérique a été testée in vitro contre le D614G-SARS-CoV-2. Les lymphocytes B (LB) mémoires CD19 + IgD-CD27± spécifiques du RBD ont été analysés en cytométrie en flux et triés en cellule unique pour séquençage des régions variables de la chaîne lourde de l’immunoglobuline.

Résultats

La réponse sérologique anti-RBD IgG et IgA était comparable aux temps précoces et tardifs de la réponse vaccinale, évoluant de façon similaire chez les patients déficients en interféron de type I et les sujets sains. La capacité de neutralisation des sérums contre le SARS-CoV-2 était également identique dans tous les groupes, et corrélait fortement avec le taux d’IgG anti-RBD, suggérant que le RBD était également la cible de la réponse neutralisante chez les patients déficients en interféron de type I. Des LB mémoires circulants spécifiques du RBD étaient retrouvés dans toutes les cohortes de patients déficients en interféron de type I au cours des 3 mois suivant la vaccination. Ceux-ci se maintenaient dans le temps et étaient encore présents entre 3 et 7 mois après la vaccination (0,18 % des LB IgD-CD27+ chez les sujets sains, 0,24 % chez les sujets avec déficit génétiques, 0,16 % chez les APS-1 et 0,26 % chez les AAB, pas de différence statistiquement significative). Le séquençage de la chaîne lourde des régions variables de l’immunoglobuline des LB mémoires spécifiques du RBD révélait l’accumulation progressive des mutations jusqu’à 7 mois chez les sujets sains, témoignant d’une réaction des centres germinatifs permettant la maturation d’affinité et la génération de lymphocytes B mémoires à longue durée de vie. Chez les patients IRF7 déficients, les LB mémoires spécifiques du RBD acquerraient progressivement des mutations de M1 à M6, et les LB mémoires spécifiques du RBD de patients TLR7 et APS-1 arboraient un nombre élevé de mutation dès M4, témoignant que même en l’absence de réponse à l’interféron de type I, le vaccin permettait la génération des LB mémoire issus des centres germinatifs, comme chez les sujets sains. Enfin, des clones partagés étaient retrouvés entre les sujets sains et les patients déficient en interféron de type I témoignant d’une réponse qualitativement normale.

Conclusion

Notre travail apporte des données rassurantes sur la vaccination de ces patients à haut risque de forme de grave de COVID-19 et suggère que l’ARNm contenu dans les vaccins n’a pas de rôle adjuvant intrinsèque.

HCV cure: an appropriate moment to reduce cannabis use in people living with HIV? (ANRS CO13 HEPAVIH data)

BACKGROUND

Thanks to direct-acting antivirals, hepatitis C virus (HCV) infection can be cured, with similar rates in HCV-infected and HIV-HCV co-infected patients. HCV cure is likely to foster behavioral changes in psychoactive substance use, which is highly prevalent in people living with HIV (PLWH). Cannabis is one substance that is very commonly used by PLWH, sometimes for therapeutic purposes. We aimed to identify correlates of cannabis use reduction following HCV cure in HIV-HCV co-infected cannabis users and to characterize persons who reduced their use.

METHODS

We used data collected on HCV-cured cannabis users in a cross-sectional survey nested in the ANRS CO13 HEPAVIH cohort of HIV-HCV co-infected patients, to perform logistic regression, with post-HCV cure cannabis reduction as the outcome, and socio-behavioral characteristics as potential correlates. We also characterized the study sample by comparing post-cure substance use behaviors between those who reduced their cannabis use and those who did not.

RESULTS

Among 140 HIV-infected cannabis users, 50 and 5 had reduced and increased their use, respectively, while 85 had not changed their use since HCV cure. Cannabis use reduction was significantly associated with tobacco use reduction, a decrease in fatigue level, paying more attention to one's dietary habits since HCV cure, and pre-HCV cure alcohol abstinence (p = 0.063 for alcohol use reduction).

CONCLUSIONS

Among PLWH using cannabis, post-HCV cure cannabis reduction was associated with tobacco use reduction, improved well-being, and adoption of healthy behaviors. The management of addictive behaviors should therefore be encouraged during HCV treatment.

La vaccination par ARNm des sujets naïfs ou convalescents de la COVID-19 permet la génération de lymphocytes B mémoires capables de reconnaître et de neutraliser les variants du SARS-CoV-2

Introduction

La mémoire immunitaire est un mécanisme qui protège les individus contre la réinfection. Cette stratégie de défense de l’organisme, qui est à la base du succès des vaccins, comprend la production d’anticorps protecteurs dans le sang ainsi que la formation de cellules à mémoire, capables de se réactiver rapidement en cellules productrices d’anticorps lors d’une nouvelle infection. Les vaccins à ARNm, codant pour la protéine Spike du SARS-CoV-2, ont été rapidement déployés dans le monde entier, avec une grande efficacité clinique. Déterminer les caractéristiques de la réponse lymphocytaire B mémoire générée par ces vaccins est d’une importance majeure, notamment dans le contexte de circulation de variants du SARS-CoV-2, porteurs de mutations dans la protéine Spike. Nous avons étudié la dynamique, l’évolution clonale, et l’affinité des cellules B à mémoire chez des patients vaccinés par le vaccin à ARNm, ainsi que leur capacité à reconnaître et à neutraliser les variants du SARS-CoV-2 dans deux cohortes longitudinales de patients, l’une infectée lors de la première vague (convalescents-vaccinés), et l’autre n’ayant pas été infectée (naïfs-vaccinés).

Patients et méthodes

Les patients infectés lors de la première vague de la pandémie ont été inclus dans l’étude MEMO-CoV2. Une partie de ces patients avec une forme sévère hospitalisée, ou une forme modérée ambulatoire ont reçu une dose de vaccin à ANR messager (BNT162b2) un an après l’infection. De façon parallèle, une cohorte de soignants, naïfs de toute infection et avec une sérologie négative, ont été vaccinés avec deux doses de vaccin à ARNm. Ces deux cohortes ont été suivies et analysées (Sérologie, Cytométrie en flux des cellules B) longitudinalement jusqu’à 2 mois après le boost vaccinal (première injection pour les convalescents, deuxième injection pour les naïfs). Les cellules B mémoires spécifiques du domaine RBD de la protéine Spike ont été isolées, triées et cultivées en cellule unique. Pour chaque cellule anti-RBD mémoire, nous avons séquencé la chaîne lourde de l’immunoglobuline et nous avons déterminé l’affinité par Biolayer-interferometry des anticorps produits contre des variants préoccupants(α, β, γ et δ). Nous avons aussi déterminé pour certains clones leur capacité à neutraliser le virus D614G (dominant lors de la première vague) et β in vitro.

Résultats

La vaccination induisait une réponse sérologique IgG anti-RBD robuste chez tous les patients analysés (n = 47). L’activité neutralisante du sérum contre le virus D614G était excellente pour tous les patients. Néanmoins, la neutralisation sérique des variants β et δ était très nettement meilleure chez les patients déjà infectés, suggérant que les plasmocytes mobilisés lors du boost vaccinal proviennent de cellules mémoires matures. L’analyse en cytométrie en flux, a mis en évidence une expansion du pool mémoires chez les patients convalescents à un niveau supérieur à celui des naïfs. L’analyse de plus de 2400 séquences de la chaîne lourde de l’immunoglobuline provenant de cellules B mémoires anti-RBD cultivés en cellule unique, a révélé que la réponse vaccinale anti-RBD mobilise des cellules peu mutées, donc nouvellement générées, chez les individus naïfs. À l’inverse les cellules mémoires mobilisées après le boost chez patients convalescents arboraient de nombreuses mutations somatiques, témoignant de la mobilisation de mémoires préexistantes. L’analyse du répertoire des cellules B mémoires montrait que sa diversité était conservée après la vaccination malgré son expansion. Nous avons ensuite analysé l’affinité de 382 anticorps monoclonaux issus cellules B mémoires mobilisées par le boost vaccinal, contre le RBD de différent variants (α, β, γ, δ, κ). L’affinité des anticorps contre la RBD sauvage était plus forte chez les convalescents que chez les naïfs et corrélait avec le nombre de mutations somatiques dans la chaine lourde de l’immunoglobuline, reflétant le processus de maturation d’affinité. Des clones de très haute affinité contre tous les RBD variants étaient détectés chez tous les individus testés, y compris chez les naïfs, ainsi que des clones neutralisant le variant β, qui a la plus grande capacité à échapper à la réponse immune.

Conclusion

Chez les patients convalescents, la vaccination amplifie un large répertoire de cellules B mémoires matures et génère des plasmocytes neutralisant les variants. Chez les individus naïfs, la vaccination induit un pool de mémoire contenant des clones neutralisants puissants contre tous les variants préoccupants actuels, dont bêta et delta. Nos résultats suggèrent qu’une troisième dose chez les sujets naïfs permettrait de différentier en plasmocytes les lymphocytes B mémoires de grande qualité générés par le schéma vaccinal initial et ainsi d’augmenter l’activité neutralisante des sérums contre les variants du SARS-CoV-2.

Bénéfice de l’ivermectine : de la gale à la COVID-19, un exemple de sérendipité

Introduction

L’âge, facteur principal de la COVID-19 sévère/mortelle, explique que les résidents des EHPAD, âgés et/ou comorbides, soient à risque. L’ivermectine (IVM), anti-parasitaire, a montré une activité antivirale anti-SARS-CoV-2 in vitro (étude australienne). La moxidectine (MOX) pourrait aussi être intéressante (demi-vie longue). Lors d’une épidémie de gale en EHPAD où les résidents ont reçu de l’IVM orale, nous rapportons son impact sur la Covid-19 survenue en parallèle.

Observation

Le 6/03/20 : patiente de 66 ans = résidente-1, EHPAD-A (Seine-et-Marne, 77), hospitalisée pour gale profuse. Incluse dans l’essai contrôlé randomisé (ECT) « gale CRUSTED ; NCT02841215 », a reçu 3 doses d’IVM (400 ou 200 μg/kg en insu ; J0-J7-J14). Trois autres résidents avaient une gale ; et résidents et personnels ont reçu IVM 200 μg/kg J0–J7 (n = 121). Retour de la résidente-1 à l’EHPAD-A le 17/03 (plan blanc).

Étude épidémiologique : Les cas probables ou confirmés (PCR) de COVID-19 de l’EHPAD-A entre 5/03 et 15/05 ont été identifiés, facteurs de risque, sévérité et mortalité précisés. Durant cette période, les infections COVID-19 et décès des autres EHPAD du 77 étaient déclarés à l’ARS. Une comparaison EHPAD-A et contrôles (EHPAD du 77 comparables en âge, effectif et tarif) était réalisée.

Étude virologique in vitro : Mesure de l’activité anti-SARS-CoV-2 de l’IVM et MOX sur cellules VeroE6 à doses croissantes (0,05–10 μM) par quantification ARN et immunofluorescence ; viabilité des cellules surveillée.

Résultats

Soixante-neuf résidents (incluant résidente-1) et 52 personnels EHPAD-A ont reçu l’IVM : âge médian résidents 90 ans (84–94), 78,3 % femmes, 98,6 % au moins une comorbidité à risque de COVID-19 sévère. 11 sujets présentaient une COVID-19 probable ou certaine (7/69 résidents et 4/52 personnels, fréquence 10,1 %). Parmi les résidents, 90,9 % (10/11) ont eu une COVID-19 minime, sans oxygène ou hospitalisation, aucun mort. Parmi les 177 EHPAD du 77, 45 étaient inclus comme contrôles, soit 3062 résidents (âge médian 86,2 ans, 77,3 % femmes). Parmi eux, 22,6 % [95 %IC 16,3-28,9] ont eu la COVID-19 vs. 1,4 % EHPAD-A avec une mortalité attribuable de 4,9 % [95 %IC 3,2-6,5] vs. 0 % EHPAD-A. Une activité antivirale majeure in vitro de l’IVM et MOX (EC₅₀ IVM 0,14 ± 0,02 μM et MOX 0,48 μM ± 0,08 μM) avec viabilité cellulaire préservée était observée.

Discussion

Tous les cas observés de COVID-19 dans l’EHPAD-A « traité » par IVM étaient mineurs, sans décès durant la période d’étude, alors que les résidents des EHPAD « contrôles » (sans IVM), appariés selon âge, effectif et niveau socio-économique, ont montré une fréquence de COVID-19 et une mortalité plus élevées. L’IVM pourrait avoir un rôle protecteur (suggéré depuis dans étude US), conforté par l’étude virologique. Malgré les limites –caractère observationnel et absence de corrélation démontrée in vitro/in vivo–, la plausibilité est suffisante pour réaliser un ECT en cluster de prévention par IVM et MOX en EHPAD.

Most chilblains observed during the COVID-19 outbreak occur in patients who are negative for COVID-19 on polymerase chain reaction and serology testing

Background

Acral lesions, mainly chilblains, are the most frequently reported cutaneous lesions associated with COVID‐19. In more than 80% of patients tested, nasopharyngeal swabs were negative on reverse transcription polymerase chain reaction (RT‐PCR) for SARS‐CoV‐2 when performed, and serology was generally not performed.

Methods

A national survey was launched on 30 March 2020 by the French Society of Dermatology asking physicians to report cases of skin manifestations in patients with suspected or confirmed COVID‐19 by using a standardized questionnaire. We report the results for acral manifestations.

Results

We collected 311 cases of acral manifestations [58.5% women, median age 25.7 years (range 18–39)]. The most frequent clinical presentation (65%) was typical chilblains. In total, 93 cases (30%) showed clinical suspicion of COVID‐19, 67 (22%) had only less specific infectious symptoms and 151 (49%) had no clinical signs preceding or during the course of acral lesions. Histology of skin biopsies was consistent with chilblains. Overall, 12 patients showed significant immunological abnormalities. Of the 150 (48%) patients who were tested, 10 patients were positive. Seven of 121 (6%) RT‐PCR‐tested patients were positive for SARS‐CoV‐2, and five of 75 (7%) serology‐tested patients had IgG anti‐SARS‐CoV‐2. Tested/untested patients or those with/without confirmed COVID‐19 did not differ in age, sex, history or acral lesion clinical characteristics.

Conclusions

The results of this survey do not rule out that SARS‐CoV‐2 could be directly responsible for some cases of chilblains, but we found no evidence of SARS‐CoV‐2 infection in the large majority of patients with acral lesions during the COVID‐19 lockdown period in France.

What is already known about this topic?

About 1000 cases of acral lesions, mainly chilblains, were reported during the COVID‐19 outbreak.

Chilblains were reported to occur in young people within 2 weeks of infectious signs, which were mild when present.

Most cases did not have COVID‐19 confirmed by reverse transcription polymerase chain reaction (RT‐PCR), and few serology results were available.

What does this study add?

Among 311 patients with acral lesions, mainly chilblains, during the COVID‐19 lockdown period in France, the majority of patients tested had no evidence of SARS‐CoV‐2 infection.

Overall, 70 of 75 patients were seronegative for SARS‐Cov‐2 serology and 114 of 121 patients were negative for SARS‐CoV‐2 RT‐PCR.

Machine learning in the clinical microbiology laboratory: has the time come for routine practice?

BACKGROUND

Machine learning (ML) allows the analysis of complex and large data sets and has the potential to improve health care. The clinical microbiology laboratory, at the interface of clinical practice and diagnostics, is of special interest for the development of ML systems.

AIMS

This narrative review aims to explore the current use of ML In clinical microbiology.

SOURCES

References for this review were identified through searches of MEDLINE/PubMed, EMBASE, Google Scholar, biorXiv, arXiV, ACM Digital Library and IEEE Xplore Digital Library up to November 2019.

CONTENT

We found 97 ML systems aiming to assist clinical microbiologists. Overall, 82 ML systems (85%) targeted bacterial infections, 11 (11%) parasitic infections, nine (9%) viral infections and three (3%) fungal infections. Forty ML systems (41%) focused on microorganism detection, identification and quantification, 36 (37%) evaluated antimicrobial susceptibility, and 21 (22%) targeted the diagnosis, disease classification and prediction of clinical outcomes. The ML systems used very diverse data sources: 21 (22%) used genomic data of microorganisms, 19 (20%) microbiota data obtained by metagenomic sequencing, 19 (20%) analysed microscopic images, 17 (18%) spectroscopy data, eight (8%) targeted gene sequencing, six (6%) volatile organic compounds, four (4%) photographs of bacterial colonies, four (4%) transcriptome data, three (3%) protein structure, and three (3%) clinical data. Most systems used data from high-income countries (n = 71, 73%) but a significant number used data from low- and middle-income countries (n = 36, 37%). Performance measures were reported for the 97 ML systems, but no article described their use in clinical practice or reported impact on processes or clinical outcomes.

IMPLICATIONS

In clinical microbiology, ML has been used with various data sources and diverse practical applications. The evaluation and implementation processes represent the main gap in existing ML systems, requiring a focus on their interpretability and potential integration into real-world settings.

Molecular testing for respiratory pathogens in sickle cell disease adult patients presenting with febrile acute chest syndrome

BACKGROUND

Differentiating acute chest syndrome (ACS) from community-acquired pneumonia (CAP) is challenging in adults presenting with major sickle cell disease (SCD) (semiological similarity, rare microbiological documentation). We aimed to assess the usefulness of nucleic acid amplification test (NAAT) for respiratory pathogens, in combination with standard bacteriological investigations, in febrile ACS adult patients presenting with major SCD.

METHODS

We performed a prospective, monocentric, observational study of 61 SCD adults presenting with febrile ACS from February 2015 to April 2016. Systematic blood, urine, and respiratory specimens were collected, before antibiotic initiation, for culture, urinary antigen tests, serology, and NAAT for respiratory pathogens.

RESULTS

A pathogen was detected in 12 febrile ACS (19.7%): four viruses (6.6%) (Rhinovirus; Influenza A/B), seven bacteria (11.4%) (S. aureus, S. pneumoniae, K. pneumoniae, L. pneumophila, M. pneumoniae), one mixed infection (1.6%) (S. aureus and Influenza B). NAAT only detected L. pneumophila in one case (serogroup 2). Apart from a significantly shorter antibiotic therapy duration (6.1 vs. 7.8 days, P=0.045), no difference was observed between undocumented and microbiologically-documented febrile ACS.

CONCLUSION

Using NAAT for the detection of respiratory pathogens in adults presenting with SCD slightly improved the microbiological diagnostic of febrile ACS, although respiratory infections are not the main etiological factor.

[Pemphigus and herpes: Multicentre survey and literature review]

BACKGROUND

Although herpes superinfection is a well-known complication of pemphigus, it has not been widely investigated.

AIM

To investigate the frequency and features of herpes infection in patients with ongoing pemphigus.

PATIENTS AND METHODS

We carried out a multicenter retrospective study between 2008 and 2016 in patients with newly diagnosed pemphigus presenting active herpes infection. Clinical, virological, immunological and therapeutic data were collated. We performed a literature review for pemphigus and herpes.

RESULTS

Among the 191 pemphigus patients, screening for herpes (PCR or culture) was carried out in 11 to 71 % of subjects, depending on the center in question. Twenty-four patients (12 women, mean age 58 years) presented at least one episode of herpes infection. The frequency of positivity ranged from 0 to 42 % by center. Twenty-one cases consisted of pemphigus vulgaris and infection occurred at a mucosal site in 19 patients. Herpes infection was identified at the time of diagnosis in 15 patients and 17 patients received no specific treatment for their pemphigus. The virus was identified using PCR in 23 cases. Ten patients subsequently received prophylactic treatment for herpes. The mean duration of follow-up was 36 months (0-89 months). Thirteen of the 24 patients had 23 relapses of pemphigus; PCR testing for herpes was performed 19 times and was positive in 6 cases (31.5 %).

CONCLUSION

Our study showed wide variation in the incidence of herpes superinfection in patients with pemphigus, reflecting the different screening approach at each center (being performed either routinely or only in the event of strong suspicion). The prognostic value of routine screening for herpes in patients with active pemphigus lesions remains to be demonstrated by further prospective investigations.

Viral kinetics analysis and virological characterization of treatment failures in patients with chronic hepatitis C treated with sofosbuvir and an NS5A inhibitor

BACKGROUND

The combination of sofosbuvir (SOF) plus an NS5A inhibitor for 12 weeks is highly efficacious in patients with chronic hepatitis C. As the costs of generic production of sofosbuvir and NS5A inhibitor are rapidly decreasing, the combination of these DAAs will be the standard treatment in most low- to middle-income countries in the future.

AIM

To identify key predictors of response that can be used to tailor treatment decisions.

METHODS

A cohort of 216 consecutive patients infected with HCV genotype 1 (1a: n = 57; 1b: n = 77), 2 (n = 4), 3 (n = 33) or 4 (n = 44) were treated with sofosbuvir (SOF) + daclatasvir (n = 176) or SOF + ledipasvir (n = 40) for 12 weeks. The viral kinetics was analysed using the biphasic model and the cure boundary was used to predict time to clear HCV.

RESULTS

The overall SVR rate was high (94.4%; n = 204), regardless of the time to viral suppression or low-level viraemia at the end of treatment. The model-based predicted HCV RNA levels at the end of treatment could not differentiate patients who did from those who did not achieve SVR. The presence of NS5A resistance-associated substitutions [position 28 (OR = 70.3, P<.001) and/or 31 (OR = 61.6, P = .002)] at baseline was predictive of virological failure in cirrhotic patients but was not associated with on-treatment viral kinetics.

CONCLUSION

This real-world study confirms the excellent results of clinical trials with therapies based on a combination of SOF plus an NS5A inhibitor. It suggests that a personalized approach including baseline NS5A inhibitor resistance testing may inform treatment decisions in cirrhotic patients.

Soluble biomarkers of immune activation and inflammation in HIV infection: impact of 2 years of effective first-line combination antiretroviral therapy

OBJECTIVES

The aim of the study was to assess the impact of rapid and sustained viral control produced by combination antiretroviral therapy (cART) on HIV-associated immune activation and inflammation.

METHODS

In this longitudinal observational study, we examined changes in interleukin-6 (IL-6), interferon-γ-inducible protein-10 (IP-10), monokine induced by interferon-γ (MIG) and soluble CD14 (sCD14) levels during 2 years of effective first-line cART. Biomarker levels before and after cART were compared with those observed in healthy subjects, using the Wilcoxon signed rank test. Elevated biomarker levels were defined with respect to values for healthy subject (mean + 2 standard deviations). Factors associated with persistently elevated biomarker levels after 2 years of cART were identified by logistic regression.

RESULTS

We included in the study 139 patients with a median HIV-1 RNA level of 4.8 log10 HIV-1 RNA copies/mL and a median CD4 cell count of 294 cells/μL at cART initiation [day 0 (D0)]. At D0, all biomarker levels were higher than in healthy subjects (P < 0.05). After 2 years of cART, IL-6, IP-10 and MIG levels fell significantly, by a median of 0.54, 420 and 1107 pg/mL, respectively (all P < 0.001), and were no longer elevated in > 75% of patients. In contrast, sCD14 levels did not change significantly (0.18 × 10(6)  pg/mL; P = 0.102) and remained elevated. Older age was associated with elevated levels of IP-10 [odds ratio (OR) 1.60 per 10 years older; P = 0.047] and MIG (OR 1.92 per 10 years older; P = 0.007) after 2 years of cART.

CONCLUSIONS

The rapid and sustained viral suppression produced by first-line cART reduced IL-6, IP-10 and MIG to normal levels, while sCD14, a marker of monocyte activation, remained elevated. High levels of IP-10 and MIG tended to persist in older patients.

Rapid plasma viral suppression in naive HIV-infected patients with high CD4 cells and low viraemia initiating a dual nucleoside reverse transcriptase inhibitor strategy: a proof-of-concept study

OBJECTIVES

To evaluate whether a dual nucleoside reverse transcriptase inhibitor (NRTI) strategy can control HIV replication in antiviral therapy (ART)-naive HIV-infected patients with a high CD4 cell count and a low viral load (VL).

METHODS

This observational study included all HIV-infected treatment-naive patients with a CD4 cell count >300 cells/mm(3), a plasma HIV RNA between 1000 copies/mL and 30,000 copies/mL and wild-type virus who initiated dual NRTI ART between January 2008 and December 2012. HIV RNA and CD4 cell count were assessed at Day 0, Week (W) 4, W12, W24 and W48. The primary endpoint was the proportion of patients with a plasma VL (pVL) <50 copies/mL at W24.

RESULTS

Twenty patients were included. The median (IQR) baseline characteristics were: time since HIV diagnosis, 25 months (8-66 months); CD4 cell count, 592 cells/mm(3) (405-798 cells/mm(3)); HIV RNA, 10,395 copies/mL (4106-16,566 copies/mL); and HIV DNA, 464 copies/10(6) peripheral blood mononuclear cells (195-1168 copies/10(6) PBMC). Nineteen patients received tenofovir/emtricitabine and one patient received abacavir/lamivudine. At W12, 88% of the patients with available data (n = 16/18, 95% CI 0.65-0.99) had a pVL <50 copies/mL. Overall, the proportion of patients with a pVL <50 copies/mL was 100% (n = 20/20, 95% CI 0.83-1.0) at W24 and 95% (n = 18/19, 95% CI 0.74-0.99) at W48 (with one patient lost to follow-up and one patient with poor treatment compliance). The median increase in CD4 cells was 83 cells/mm(3) (40-310 cells/mm(3)). There was no discontinuation of antiretroviral therapy for any reason such as lack of efficacy or toxicity.

CONCLUSIONS

This pilot study suggests that, in patients with a high CD4 cell count and a low VL, a dual NRTI strategy may represent a potentially effective treatment strategy to control HIV replication. This needs to be confirmed in larger controlled clinical studies.

T-01: Taux élevé d’infections respiratoires virales chez les patients hospitalisés et le personnel soignant, hiver 2014

Introduction – objectifs

Déterminer la prévalence des infections respiratoires virales symptomatiques ou non parmi les patients et les soignants d’un service de maladies infectieuses. Rechercher les facteurs associés à la transmission nosocomiale.

Matériels et méthodes

Les patients hospitalisés entre le 15/01 (S1) et le 30/03/14 (S10) sont inclus prospectivement, avec recueil de données cliniques, prélèvement nasopharyngé tous les 2 à 5 jours pour PCR multiplex à la recherche de 22 pathogènes. Les soignants ont un prélèvement à S5 et en cas de symptôme. Une sérologie est faite chez les patients symptomatiques et le personnel, avec contrôle à S4.

Résultats

Après 7 semaines sur 10 de l’étude toujours en cours, il y a eu 35 infections respiratoires chez 44 % (28/64) du personnel. Un virus était présent dans 25 des 35 prélèvements (71 %) : 12 coronavirus (48 % : 7 OC43, 3 NL63, 2 HKU1), 6 PIV4 (24 %), 5 influenza A (20 %, dont 3 H1N1pdm09), 5 rhinovirus (20 %) et 1 VRS. Dans 4 prélèvements (11 %) plus d’un virus était identifié.

Sur 105 patients inclus, 45 avaient des signes d’infection respiratoire (44 %), parmi lesquels 27 prélèvements étaient positifs (60 %) pour 34 virus : 5 coronavirus (12 % : 2 OC43, 2 NL63, 1 229E), 2 PIV (1 PIV1 et 1 PIV2), 16 influenza A (47 %, dont 8 H1N1pdm09), 10 rhinovirus (29 %) et 1 hMPV. Dans 7 prélèvements (26 %) plus d’un virus était identifié.

Les taux de vaccination anti-grippale étaient de 70 % (45/64) chez les soignants (mais 42 %, 8/19, chez les étudiants hospitaliers).

Quelques cas de potentielle transmission dans le service sur des critères chronologiques et virologiques ont été identifiés.

Conclusion

Les infections virales respiratoires sont fréquentes chez les soignants en période hivernale, avec un risque de transmission aux patients et aux autres soignants.

High level of HIV-1 resistance in patients failing long-term first-line antiretroviral therapy in Mali

OBJECTIVES

In resource-limited settings, few data are available on virological failure after long-term first-line antiretroviral therapy. This study characterized the genotypic resistance patterns at the time of failure after at least 36 months of a first-line regimen in Mali, West Africa.

METHODS

Plasma samples from 84 patients who were receiving first-line antiretroviral treatment and with an HIV-1 RNA viral load (VL) >1000 copies/mL were analysed. Genotypic resistance testing was performed and HIV-1 drug resistance was interpreted according to the latest version of the National Agency for HIV and Hepatitis Research algorithm.

RESULTS

At the time of resistance testing, patients had been treated for a median of 60 months (IQR 36-132 months) and had a median CD4 cell count of 292 cells/mm(3) (IQR 6-1319 cells/mm(3)), a median HIV-1 RNA level of 28266 copies/mL (IQR 1000-2 93 495 copies/mL) and a median genotypic susceptibility score of 1 (IQR 1-4). The prevalence of nucleoside reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations was 78% and 82%, respectively. Viruses were resistant to at least one drug in 92% of cases. Although etravirine and rilpivirine were not used in the first-line regimens, viruses were resistant to etravirine in 34% of cases and to rilpivirine in 49% of cases. The treatment duration, median number of NRTI and NNRTI mutations and some reverse transcriptase mutations (T215Y/F/N, L210W, L74I, M41L and H221Y) were associated with the VL at virological failure.

CONCLUSIONS

This study demonstrated a high level of resistance to NRTIs and NNRTIs, compromising second-generation NNRTIs, for patients who stayed on long-term first-line regimens. It is crucial to expand the accessibility of virological testing in resource-limited settings to limit the expansion of resistance and preserve second-line treatment efficacy.

Genetic barrier to the development of resistance to rilpivirine and etravirine between HIV-1 subtypes CRF02_AG and B

OBJECTIVES

It has been demonstrated for some drugs that the genetic barrier, defined as the number of genetic transitions and/or transversions needed to produce a resistance mutation, can differ between HIV-1 subtypes. We aimed to assess differences in the genetic barrier for the evolution of resistance to the second-generation non-nucleoside reverse transcriptase inhibitors etravirine and rilpivirine in subtypes B and CRF02_AG in antiretroviral-naive patients.

METHODS

An analysis was undertaken of 25 substitutions associated with etravirine and rilpivirine resistance at 12 amino acid positions in 267 nucleotide sequences (136 HIV-1 B and 131 HIV-1 CRF02_AG subtypes) of the reverse transcriptase gene.

RESULTS

The majority (7/12) of amino acid positions studied were conserved between the two HIV-1 subtypes, leading to a similar genetic barrier. Different predominant codons between the subtypes were observed in 5/12 positions (90, 98, 179, 181 and 227), with an effect on the calculated genetic barrier only at the V179D and V179F codons (2.5 versus 3.5 for V179D, and 2.5 versus 5 for V179F, respectively, for subtype B versus subtype CRF02_AG).

CONCLUSIONS

The majority of amino acids involved in etravirine and rilpivirine resistance showed a high degree of conservation of the predominant codon between the B and CRF02_AG subtypes. For rilpivirine, the genetic barrier was the same between the two subtypes. Nevertheless, subtype CRF02_AG showed a higher genetic barrier to acquiring mutations V179D and V179F (mutations associated with resistance to etravirine) compared with subtype B, suggesting that it would be more difficult to produce resistance to etravirine in the CRF02_AG subtype than the B subtype.

[The usefulness of elastase measurement in the sperm for the diagnosis of urogenital male inflammation and infection]

BACKGROUND

Genital tract inflammation is a frequent cause of infertility among men, usually clinically silent with only leukocytospermia defined as the presence of white blood cells (WBC)>1.106/ml in semen. During the inflammation process, granulocytes discharge large amounts of proteases such as elastase. The elastase linked to its inhibitor in the form of a complex the elastase α1-protease inhibitor in semen is suggested as a potential marker of genital tract inflammation.

AIM

To assess the measurement of elastase as a biomarker of genital tract inflammation by comparing this technique with the detection of leukocytospermia according to the WHO guidelines.

METHODS

This study interested 83 infertile men attending the andrology center for semen analysis. Leukocytospermia was assessed by a peroxydase test and elastase concentration by immunoassay in the seminal plasma.

RESULTS

An elevated elastase was found in 38% of men. A similarity was found between leukocytospermia and elastase in 79% of cases, kappa coefficient concordance with leukocytospermia is good (0.78). The sensitivity of the elastase is 100%, the specificity= 75%. The positive predictive value is 47%, the negative predictive value is 100% with a Youden index=0.75. All patients with leukocytospermia>1.106/ml had an elastase>250ng/ml, 73% of them a concentration>1000 ng/ml. In the group of patients with no leucocytospermia, 75% had elastase<250ng/ml, 21% had concentration between 250 and 1000ng/ml and 4% (3 patients) a concentration>1000ng/ml.

CONCLUSION

Seminal elastase is a more sensitive marker than leucocytospermia in the diagnosis of male urogenital inflammation and infection.

Switch from etravirine twice daily to once daily in non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistant HIV-infected patients with suppressed viremia: the Monetra study

BACKGROUND

Etravirine (ETR) is recommended as twice-daily dosing in pretreated patients. There are no data regarding the use of ETR once daily in HIV-experienced patients with prior resistance to first-generation non-nucleoside reverse transcripase inhibitors (NNRTIs).

OBJECTIVES

To evaluate the capacity of once-daily ETR to maintain suppressed viremia over 48 weeks after switching from ETR twice daily in NNRTI-experienced patients.

METHODS

In this pilot open-label study, patients with plasma viral load (pVL) <50 copies/mL on a stable ETR 200 mg bid regimen were enrolled to switch to ETR 400 mg qd and followed up over 48 weeks. The primary endpoint was the proportion of patients with pVL <50 copies/mL at week 24. Secondary endpoints included the rate of pVL< 50 copies/mL at week 48, ETR pharmacokinetic parameters, and tolerability and resistance profile.

RESULTS

Twenty-four patients were included. They had extensive antiretroviral treatment for a median of 14 years (range, 1-19). All except for 2 had prior resistance to NNRTIs. Seven patients discontinued ETR once daily prior to week 48 for virological failure (3), protocol deviation (3), and side effects (1). At week 24, 95% of patients maintained pVL< 50 copies/mL (95% CI, 78.4-99.7) and 85% at week 48 (95%CI, 65.6-95.8). Two of the 3 patients with virological failure had ETR resistance mutations prior to initiation. The median ETR C(trough) level remained stable after switching from twice daily 515 ng/mL (340-758) to once daily 422 ng/mL (264-655).

CONCLUSION

These results suggest that ETR is effective as a once-daily regimen in patients with prior NNRTI experience when HIV is sensitive to ETR. The stability of C(trough) concentrations on a once-daily regimen confirms the once-daily profile of the drug in experienced patients.

[Neisseria meningitidis invasive infections in children in Tunis: about 79 cases]

We conducted a retrospective study of meningococcal invasive diseases (MID) contracted in children in Tunis between January 1997 and January 2006. The purpose of this study is to specify the clinical, epidemiological, therapeutic and evolutionary features of these infections and to determine antimicrobial susceptibility and the antigenic formula of N. meningitidis isolates. During the study period, we have collected 79 cases of MID arising in children aged 3 days to 11 years. The majority of children's were less than of 4 years (57.3%). We note a frequency of the MID in winter and in spring. The most frequent clinical shape was meningitis (53%). Twenty one patients (26.6%) had a fulminant meningococcal disease. In our series, the rate of lethality was equal to 17.7%. Among the 46 meningococcal isolates, the most frequent serogroup was the B (73%) followed by C and A. A high heterogeneousness of the antigenic formulae was observed The most frequent phenotype was NT: NST for the group B isolates and 4:P1.13 for the group C ones. N meningitidis with reduced susceptibility to penicillin and to amoxicillin account for 54% and 10% of all isolates respectively. The cefotaxim and the rifampin were uniformly active.

[Use of the rapid antigen detection test in group A streptococci pharyngitis diagnosis in Tunis, Tunisia]

The aims of this study were to determine the contribution of commercial rapid antigen detection test (RADT) in the rapid diagnosis of pharyngitis caused by group A streptococci. A total of 292 children with pharyngitis was included. A duplicate throat swabs was taken simultaneously from each patient. One of them was used for RADT achievement and the other for culture. When cultures were positive, a semi-quantitative evaluation was done. Throat culture and RADT were positive in 59 and 72 cases respectively. Fifty four specimens were positive simultaneously with RADT and culture and 215 specimens were negative using both methods. Eighteen specimens were positive only with RADT, 5 of them were treated by amoxicillin. Regarding to the group of patients with a negative RADT and a positive culture (5 cases), all of them had a culture evaluation at "+" or "++". Specificity and sensibility of the RADT were 92.2% and 91.5% respectively. RADT use by physicians can reduce antibiotic prescription among paediatric population. Because of the high specificity of RADT, therapeutic decisions can be made on the basis of a positive test.

[Chronic cor pulmonale caused by hydatid embolism complicating hepatic hydatid cyst]

An hydatid cyst of the left lobe of the liver, associated with right heart failure, was diagnosed in a 61-year-old man presenting with dyspnoea. Doppler echocardiography combined with cardiac catheterization demonstrated the presence of pulmonary precapillary hypertension. Pulmonary perfusion scintigraphy with Technetium-labelled albumin microspheres demonstrated multiple pulmonary embolisms, leading to a diagnosis of postembolic chronic cor pulmonale. Due to the absence of thrombophlebitis and ultrasound signs of an intracaval hydatid membrane, floating at the level of the cyst of the left lobe of the liver, the diagnosis of parasitic postembolic chronic heart pulmonale, due to fistulization of an hepatic hydatid cyst into the inferior vena cava, was established. Only chemotherapy was proposed in this patient due to dissemination of the hydatid material in the lungs.