Understanding the immune responses elicited by SARS-CoV-2 infection is critical in terms of protection against reinfection and, thus, for public health policy and vaccine development for COVID-19. In this study, using either live SARS-CoV-2 particles or retroviruses pseudotyped with the SARS-CoV-2 S viral surface protein (Spike), we studied the neutralizing antibody (nAb) response in serum samples from a cohort of 140 SARS-CoV-2 qPCR-confirmed infections, including patients with mild symptoms and also more severe forms, including those that required intensive care. We show that nAb titers correlated strongly with disease severity and with anti-spike IgG levels. Indeed, patients from intensive care units exhibited high nAb titers; conversely, patients with milder disease symptoms had heterogeneous nAb titers, and asymptomatic or exclusive outpatient-care patients had no or low nAbs. We found that nAb activity in SARS-CoV-2-infected patients displayed a relatively rapid decline after recovery compared to individuals infected with other coronaviruses. Moreover, we found an absence of cross-neutralization between endemic coronaviruses and SARS-CoV-2, indicating that previous infection by human coronaviruses may not generate protective nAbs against SARS-CoV-2. Finally, we found that the D614G mutation in the spike protein, which has recently been identified as the current major variant in Europe, does not allow neutralization escape. Altogether, our results contribute to our understanding of the immune correlates of SARS-CoV-2-induced disease, and rapid evaluation of the role of the humoral response in the pathogenesis of SARS-CoV-2 is warranted.

This cross-sectional study aimed to investigate, during a short period between 2000 and 2001, in a large population of patients with chronic hepatitis C, the epidemiological characteristics of hepatitis C virus (HCV) genotypes in France. Data from 26 referral centres, corresponding to 1769 patients with chronic hepatitis C were collected consecutively during a 6-month period. HCV genotyping in the 5'-non-coding region (NCR) was performed in each center using the line probe assay (LiPA, in 63% of cases), sequencing (25%) or primer-specific polymerase chain reaction (PCR) (12%). HCV genotypes 1a, 1b, 2, 3, 4, 5, non-subtyped 1 and mixed infection were found in 18, 27, 9, 21, 9, 3, 11 and 1% of our population, respectively. HCV genotype distribution was associated with gender, age, source and duration of infection, alanine aminotransferase (ALT) levels, cirrhosis, alcohol consumption, hepatitis B virus (HBV) and human immunodeficiency virus (HIV) coinfection. In multivariate analysis, only the source of infection was the independent factor significantly associated with genotype (P = 0.0001). In conclusion, this study shows a changing pattern of HCV genotypes in France, with i.v. drug abuse as the major risk factor, an increase of genotype 4, and to a lesser extent 1a and 5, and a decrease of genotypes 1b and 2. The modification of the HCV genotype pattern in France in the next 10 years may require new therapeutic strategies, and further survey studies.

Staphylococcus aureus nasal carriage is a well-defined risk factor of infection with this bacterium. The increased risk of S. aureus infection in nasal carriers is supported by the fact that the strains isolated from both colonization and infection sites are indistinguishable in most of the cases. Persistent nasal carriage seems to be associated with an increased risk of infection and this status could be defined now in clinical routine by using one or two quantitative nasal samples. There is evidence for supporting the detection of nasal carriage of S. aureus in patients undergoing cardiac surgery and in those undergoing hemodialysis in order to implement decolonization measures. More studies are needed to determine which carriers have the highest risk of infection and why decolonization strategies failed to reduce S. aureus infection in some other groups of patients.

The type III secretion system (TTSS) of Pseudomonas aeruginosa was characterized genetically and phenotypically in 92 epidemiologically unrelated bacteremic strains. Four groups of strains (TTSS types) were defined according to the level of type III protein secretion and kinetics of cytotoxicity. Type 1 strains (n=26) were highly and rapidly cytotoxic and secreted ExoU, type 2 strains (n=48) exhibited slower cytotoxic rates and expressed ExoS but not ExoU, type 3 strains (n=14) were poorly cytotoxic, and type 4 strains (n=4) were not cytotoxic. Type 3 and 4 strains did not have detectable secretion phenotype; however, some type 4 strains were able to reach a level of cytotoxicity similar to that of type 1 and type 2 strains when complemented in trans by a functional exsA gene. A statistically significant association (P<.001) was found between TTSS types and detection of the mutually exclusive exoU and exoS genes. In addition, 24 of 25 serotype O:1, O:10, and O:11 strains contained exoU, whereas 54 of 55 serotype O:3, O:4, O:6, O:12, and O:16 strains contained exoS (P<.001). Our results demonstrate correlations among exoU or exoS genotype, TTSS phenotype, and O serotype in bacteremic P. aeruginosa isolates.

Legionella viability was monitored during heat shock treatment at 70°C by a flow cytometric assay (FCA). After 30 min of treatment, for 6 of the 12 strains tested, the FCA still detected 10 to 25% of cells that were viable but nonculturable (VBNC). These VBNC cells were able to produce ATP and to be resuscitated after culture on amoebae.Legionellae are widespread in natural and manmade aquatic habitats. Sources of contamination are aerosols from showerheads, air-cooling towers, and other systems distributing water. To prevent outbreaks, surveillance of Legionella environmental contamination by use of culture methods has been set up for hot sanitary water systems in collective settings such as hospitals, hotels, and thermal spas (4). However, the findings of environmental surveillance do not always correlate with the occurrence of Legionnaires' disease, since the concentration of Legionella bacteria in environmental samples is largely underestimated when culture on GVPC medium (8,11,12), the reference method required by current norms (1, 16), is used. The existence of viable but nonculturable (VBNC) bacteria (13,21,24), which reduce the sensitivity of culture-based assays, has been demonstrated. Analysis of membrane integrity in order to distinguish between viable and dead cells in various bacterial species has been proposed (2, 14, 17, 19); some of these assays are based on double staining combining Syto 9 and propidium iodide (PI) (6, 9, 26). To date, only three studies dealing with the detection of Legionella cells by flow cytometry have been reported (15,27,29), and none of them analyzed the presence of VBNC cells, which was undertaken in this study.The flow cytometric assay (FCA) was performed on a BD FACSCanto II flow cytometer (Becton Dickinson Biosciences, Le Pont-de-Claix, France). A threshold was applied on the FL1 channel to eliminate background noise, and analyses were performed at a low flow rate setting. The concentrations of the two dyes were adjusted for the optimal discrimination of green-and red-fluorescing bacteria. One microliter of 2.3 mM Syto 9 and 5 l of 1-mg/ml PI (Invitrogen SARL, Cergy Pontoise, France) were used for cell staining. A cytogram was generated for each different Legionella strain; unstained cells and double staining of sterilized water were used to define the background noise (data not shown).During a heat shock treatment from 0 to 60 min at 70°C, the concentration of dead cells increased proportionally with the duration of heat exposure. As shown for Legionella pneumophila serogroup 1 (sg 1) in Fig. 1, the bacteria could be segregated within three regions: dead cells stained with PI were located in the P1 region (Fig. 1, dot plot at 60 min); bacteria with intact membranes that were stained with Syto 9 were used to delineate the P2 region (Fig. 1, dot plot at 0 min); and a third population, located in the P3 region and appearing as early as 1 min after the beginning of the heat shock, represented an intermediate physiological state that could correspond to cells that were st...

In this study, we systematically investigated the resistance mechanisms to ␤-lactams, aminoglycosides, and fluoroquinolones of 120 bacteremic strains of Pseudomonas aeruginosa. Pulsed-field gel electrophoresis genotyping showed that 97 of these strains were represented by a single isolate, 10 by 2 and 1 by 3 clonally related isolates, respectively. Seventy-five percent (90 out of 120) of the bacteremic P. aeruginosa strains displayed a significant resistance to one or more of the tested antimicrobials (up to 11 for 1 strain). These strains were found to harbor a great diversity of resistance mechanisms (up to 7 in 1 strain), leading to various levels of drug resistance. Interestingly, 11 and 36% of the isolates appeared to overproduce the MexAB-OprM and MexXY-OprM efflux systems, respectively. Altogether, our results show that P. aeruginosa may accumulate intrinsic (overproduction of cephalosporinase AmpC, increased drug efflux, fluoroquinolone target mutations, and deficient production of porin OprD) and exogenous (production of secondary ␤-lactamases and aminoglycoside-modifying enzymes) resistance mechanisms without losing its ability to generate severe bloodstream infections. Consequently, clinicians should be aware that multidrug-resistant P. aeruginosa may remain fully pathogenic.

The molecular diagnosis of respiratory infection can be performed using different commercial multiplex-based PCR kits whose performances have been previously compared individually to those of conventional techniques. This study compared the practicability and the diagnostic performances of six CE-marked kits available in 2011 on the French market, including 2 detecting viruses and atypical bacteria (from Pathofinder and Seegene companies) and 4 detecting only viruses (from Abbott, Genomica, Qiagen and Seegene companies). The respective sensitivity, specificity, accuracy and agreement of each multiplex technique were calculated by comparison to commercial duplex PCR tests (Argene/bioMérieux) used as gold standard. Eighty-eight respiratory specimens with no pathogen (n = 11), single infections (n = 33) or co-infections (n = 44) were selected to cover 9 viruses or groups of viruses and 3 atypical bacteria. All samples were extracted using the NUCLISENS® easyMAG™ instrument (bioMérieux). The overall sensitivity ranged from 56.25% to 91.67% for viruses and was below 50% with both tests for bacteria. The overall specificity was excellent (>94% for all pathogens). For each tested kit, the overall agreement with the reference test was strong for viruses (kappa test >0.60) and moderate for bacteria. After the extraction step, the hands-on time varied from 50 min to 2h30 and the complete results were available in 2h30 to 9 h. The spectrum of tested agents and the technology used to reveal the PCR products as well as the laboratory organization are determinant for the selection of a kit.

These results emphasize the need for applying various infection control measures to prevent colonization of patients with P. aeruginosa, including strategies to limit the potential of sinks from acting as a source or reservoir for this bacterium.