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Journal: Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases


The COVID-19 pandemic caused by SARS-CoV-2 remains a significant issue for global health, economics and society. A wealth of data has been generated since its emergence in December 2019 and it is vital for clinicians to keep up with this data from across the world at a time of uncertainty and constantly evolving guidelines and clinical practice.


To detect possible SARS-CoV-2 RNA contamination of inanimate surfaces in areas at high risk of aerosol formation by patients with COVID-19.


Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Due to the overwhelming use of SARS-CoV-2 RT-PCR tests worldwide, availability of test kits has become a major bottleneck, while the need to increase testing throughput only rises. We aim to overcome these challenges by pooling samples together, performing RNA extraction and RT-PCR in pools.


Weekly monitoring of European all-cause excess mortality, the EuroMOMO network, observed high excess mortality during the influenza B/Yamagata dominated 2017/18 winter season, especially among elderly. We describe all-cause excess and influenza-attributable mortality during the season 2017/18 in Europe.


It was recently suggested that Ibuprofen might increase the risk for severe and fatal COVID-19 disease and should therefore be avoided in this patient population. We aimed to evaluate whether ibuprofen use in patients with COVID-19 was associated with more severe disease, compared to patients using paracetamol or no antipyretics.


Non-alcoholic fatty liver disease (NAFLD) is a severe liver disease that is increasing in prevalence with the worldwide epidemic of obesity and its related insulin-resistance state. A ‘two-hit’ mechanism has been proposed; however, the complete physiopathogenesis remains incompletely understood. Evidence for the role of the gut microbiota in energy storage and the subsequent development of obesity and some of its related diseases is now well established. More recently, a new role of gut microbiota has emerged in NAFLD. The gut microbiota is involved in gut permeability, low-grade inflammation and immune balance, it modulates dietary choline metabolism, regulates bile acid metabolism and produces endogenous ethanol. All of these factors are molecular mechanisms by which the microbiota can induce NAFLD or its progression toward overt non-alcoholic steatohepatitis.

Concepts: Gut flora, Nutrition, Obesity, Metabolic syndrome, Liver disease, Non-alcoholic fatty liver disease, Fatty liver, Steatosis


Clin Microbiol Infect Epidemiological data on staphylococcal scalded skin syndromes (SSSS), including bullous impetigo (BI) and generalized exfoliative syndrome (GES), are scarce. To better characterize SSSS and associated Staphylococcus aureus strains, we conducted a retrospective study of 349 cases collected in France between 1997 and 2007 by the National Reference Centre of Staphylococci. Our results showed a stationary evolution of SSSS cases, with a heterogeneous distribution of cases in France. Although notification was not exhaustive, we estimated an incidence of 0.56 cases/year/million inhabitants, in accordance with previous studies conducted in France and Europe, with a median age of 2 years old and sex ratios of 1. A seasonal effect was observed, with a higher GES/BI ratio in autumn compared with other seasons, which could be explained by the impact of viral co-infection. Genetic analysis of S. aureus strains showed that accessory gene regulator (agr) 4, exfoliative toxin A (eta) and B (etb) genes, staphylococcal and enterotoxin-like O (selo) gene and agr4 etb selo profiles were predominantly associated with GES, whereas agr2 eta and agr4 eta selo were more frequently observed with BI. Only one methicillin-resistant strain was found. Protein A (spa) typing identified two main genotypes: spa clonal complex (CC) 159/sequence-type (ST) 121 (75%) and spaCC346/ST15 (18%). spaCC159 was mainly associated with agr4 eta etb selo, agr4 eta selo and agr4 etb selo, and spaCC346 was mainly associated with agr2 eta, suggesting that French SSSS cases are caused by these two main lineages. However, in a multivariate analysis, only etb was independently associated with GES.

Concepts: Bacteria, Microbiology, Staphylococcus aureus, Staphylococcus, Skin, Coagulase, Staphylococcaceae, Staphylococcal scalded skin syndrome


The 2019 novel coronavirus (SARS-CoV-2) is a new human coronavirus which is spreading with epidemic features in China and other Asian countries with cases reported worldwide. This novel Coronavirus Disease (COVID-19) is associated with a respiratory illness that may cause severe pneumonia and acute respiratory distress syndrome (ARDS). Although related to the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS), COVID-19 shows some peculiar pathogenetic, epidemiological and clinical features which have not been completely understood to date.


We assessed the persistence of anti-HBs antibody and immune memory in a cohort of 571 teenagers vaccinated against hepatitis B as infants, 17 years earlier. Vaccinees were followed-up in 2003 and in 2010, i.e. 10 years and 17 years after primary vaccination, respectively. When tested in 2003, 199 vaccinees (group A) had anti-HBs <10 mIU/ml and were boosted, 372 (group B) were not boosted because they had anti-HBs ≥10 mIU/ml (n=344) or refused booster (n=28) despite anti-HBs <10 mIU/ml. In 2010, 72.9% (416/571) participants had anti-HBs ≥10 mIU/ml (67.3% in group A vs 75.8% in group B; p=0.03).The geometric mean concentrations (GMCs) were similar in both groups. Between 2003 and 2010, anti-HBs concentrations in previously boosted individuals markedly declined with GMC dropping from 486 to 27.7 mIU/ml (p<0.001). Fifteen vaccinees showed a markedly increase of antibody possibly due to natural booster. In 2010, 96 individuals (37 of group A and 59 of group B) with anti-HBs <10 mIU/ml were boosted; all vaccinees of the former group and all but two of the latter had an anamnestic response. Post-booster GMC was higher in group B (895.6 vs 492.2 mIU/ml: p=0.039). This finding shows that the immune memory for HBsAg persists beyond the time at which anti-HBs disappears, conferring long-term protection. This article is protected by copyright. All rights reserved.

Concepts: Immune system, Antibody, Vaccination, Immunology, Humoral immunity, Immunity, Smallpox, Inoculation


Granulomas may develop as a response to a local antigenic trigger, leading to the activation of macrophages and T lymphocytes. Primary immune deficiency (PID) is associated with the development of extensive cutaneous granulomas, which etiology remains unknown. We performed High-Throughput Sequencing of the transcriptome of cutaneous granuloma lesions on two consecutive index cases and RT-PCR in a third consecutive patient. The RA27/3 vaccine strain of Rubella virus - the core component of a universally used pediatric vaccine - was present in the cutaneous granuloma of these three out of three consecutive PID patients. Controls included the healthy skin of two patients, non-granulomatous cutaneous lesions of patients with immunodeficiency, and skin biopsy samples of healthy individuals and were negative. Expression of viral antigens was confirmed by immunofluorescence. Persistence of the Rubella vaccine virus was also demonstrated in granuloma lesions sampled 4 to 5 years earlier. The persistence of rubella virus vaccine strain in three out of three consecutive cutaneous granuloma patients with PID strongly suggests a causal association between RV and granuloma in this setting. This article is protected by copyright. All rights reserved.

Concepts: HIV, Immune system, Antibody, Vaccine, Anatomical pathology, Immunodeficiency, Copyright, Primary immunodeficiency