Kinetics of SARS-CoV-2-Neutralising Antibodies of Residents of Long-Term Care Facilities.

INTRODUCTION: Elderly residents of nursing homes (NHs) and long-term care units (LTCUs) have been shown to have a high risk of mortality and morbidity in cases of SARS-CoV-2 infection. The objective of this study was to examine the kinetics of neutralizing antibodies (NAbs) directed against the SARS-CoV-2 virus in residents of the NH and LTCU units of our University Hospital who were identified with positive serology after the first epidemic outbreak. MATERIALS AND METHODS: The participants included were sampled every three months for qualitative serological testing, as well as quantitative testing by neutralization tests using retroviral particles containing the S glycoprotein of SARS-CoV-2. Vaccination using the Comirnaty (Pfizer BNT162b2) vaccine begun before the last serological follow-up. RESULTS: The median NAb titer in June 2020 was 80 [40; 60] versus 40 [40; 160] three months later, showing a statistically significant decline (p < 0.007), but remained stable between the three- and six-month timepoints (p = 0.867). By nine months after vaccination, we observed a significant difference between vaccinated residents known to have positive serology before vaccination (SERO+, Vacc+) and those vaccinated without having previously shown COVID-19 seroconversion (SERO-, Vacc+), the latter group showing similar titers to the SERO+, Vacc- participants (p=0.166). The median antibody titer in SERO+, Vacc+ patients increased 15-fold following vaccination. DISCUSSION: Humoral immunity against SARS-CoV-2 appears to be persistent in elderly institutionalized patients, with a good post-vaccination response by residents who had already shown seroconversion but a notably diminished response by those who were seronegative before vaccination. To evaluate immunity in its entirety and elaborate a sound vaccination strategy, the cellular immune response via T cells specific to SARS-CoV-2 merits analysis, as this response is susceptible to being affected by immunosenescence.

BK polyomavirus in the urine for follow-up of kidney transplant recipients.

OBJECTIVES: After kidney transplantation, human BK polyomavirus (BKPyV) can induce a progressive disease, in three stages: viruria, viraemia, and then nephropathy after a few months of viral replication. Therapeutic intervention is recommended when BKPyV is detected in the plasma. The objective of our study was to assess urinary BKPyV nucleic acid test as a predictor for developing viraemia. METHODS: We first defined a viruria threshold based on 393 time-matched urine and plasma samples collected after kidney transplantation; to validate this threshold, we followed-up a cohort of 236 kidney transplant patients. RESULTS: A BKPyV viruria threshold of 6.71 log10 copies/mL best discriminated between plasma-positive and plasma-negative patients (sensitivity 90.9% (95% CI 86.5-95); specificity 90.3% (95% CI 86.3-94.3); area under the curve 0.953 (95% CI 0.933-0.974). In the validation cohort, the risk of developing BKPyV viraemia at 1 year was 16.5% (39/236) and rose to 90.7% (39/43) if BKPyV viruria remained above the threshold of 6.71 for more than 1 month. CONCLUSIONS: Sustained BKPyV viruria is a reliable, early marker of patients at high risk of developing BKPyV viraemia. This marker should alert the clinician early, and thus allow timely therapeutic intervention.

Characterization of a multidrug-resistant Klebsiella pneumoniae ST607-K25 clone responsible for a nosocomial outbreak in a neonatal intensive care unit.

PURPOSE: Multidrug-resistant Klebsiella pneumoniae strains are regularly involved in hospital outbreaks. This study describes an ESBL-producing K. pneumoniae clone (ST607-K25) responsible for a nosocomial outbreak in a neonatal intensive care unit. METHODOLOGY: Fourteen strains isolated from 13 patients were included. Antimicrobial susceptibility testing was performed by the agar diffusion method. A clonal link was first investigated by fingerprinting (ERIC-PCR and REP-PCR) then confirmed by MLST. Characterization was performed by molecular detection and identification of several drug resistance and virulence determinants. RESULTS: All strains expressed the same antibiotype, combining ESBL production, fluoroquinolones and aminoglycoside resistance, except for one which remained susceptible to fluoroquinolones. Fingerprinting methods confirmed the clonal link and MLST identified a ST607 clone. Molecular investigations revealed: (I) genes encoding for two narrow-spectrum beta-lactamases (SHV-1 and TEM-1) and an ESBL (CTX-M-15); (II) absence of any chromosomal mutation in quinolone resistance-determining- regions (QRDR) of gyrA/gyrB and parC/parE genes; (III) genes encoding for three plasmid-mediated quinolone-resistance (PMQR) determinants: oqxAB (14/14), aac(6')-Ib-cr (14/14) and qnrB (13/14); (IV) production of a K25 capsule; and (V) carriage of three genes encoding for virulence factors: mrkD (type 3 fimbriae) (14/14), ybts (yersiniabactin) (12/14) and entB (enterobactin) (14/14). CONCLUSION: We described a multidrug-resistant Kp ST607 clone responsible for a nosocomial outbreak in vulnerable and premature newborns. Molecular investigations allowed us to identify several resistance factors responsible for ESBL production (CTX-M-15) and quinolone resistance (three PMQR determinants). The detection of a gene (ybtS) belonging to the high-pathogenicity island yersiniabactin could partly explain its high colonization and diffusion potential.

Limited efficacy of nontreponemal test combined with treponemal test in the initial syphilis screening algorithm.

PURPOSE: Various syphilis screening algorithms have been proposed and are now used by many clinical laboratories following the introduction of automated treponemal tests (TTs). In France, the diagnosis of syphilis is based on a TT combined with a nontreponemal test (NTT). The objective of this study was to evaluate the diagnostic impact of NTT on initial syphilis screening at the Amiens University Hospital between January 2013 and December 2016. METHODOLOGY: Serum samples sent for syphilis testing were analysed using a treponemal enzyme immunoassay (Siemens IMMULITE 2000 Syphilis Screen) combined with a nontreponemal test. Enzyme immunoassay (EIA)-reactive and/or nontreponemal-reactive samples were titrated to endpoint using the Treponema pallidum particle agglutination test (TPHA). Complementary tests, such as line immunoassay, and medical charts were reviewed to categorize reactive samples into positive or negative syphilis contacts. RESULTS: Among 15 523 initial screening samples, 148 samples (0.95 %) were reactive with the combined TT and NTT, and 335 (2.16 %) and 66 (0.42 %) were reactive with TT or NTT only. Analysis of the 66 discordant results between TT and NTT showed that only 4 sera were reactive with a second-line TPHA, but these results were not confirmed by line immunoassay and patient characteristics. CONCLUSION: The results of this study show that the combination of NTT and TT for initial screening does not provide any diagnostic gain, but represents additional laboratory work time.

Multicenter performance evaluation of the Unyvero IAI cartridge for detection of intra-abdominal infections.

Intra-abdominal infections (IAIs) are one of the most common type of infections in patients with sepsis and an important cause of death in intensive care units. Early detection and treatment are necessary to reduce patient complications and improve outcomes. The Unyvero IAI Application (Curetis GmbH) is the first automated assay to rapidly and simultaneously identify a large panel of bacteria, fungi, toxins, and antibiotic resistance markers directly from IAI-related samples. The assay was evaluated in four European clinical laboratories in comparison to routine microbiological practices. A total of 300 clinical samples were tested with an overall sensitivity of 89.3% and specificity of 99.5%, while time to results was reduced by an average of about 17 h compared to identification (ID) results and 41 h compared to full antibiotic susceptibility testing (AST) results. The Unyvero IAI was able to detect additional microorganisms compared with culture, in particular anaerobes, with most detections confirmed by sequencing. The most frequent resistance markers detected were mecA/mecC (n = 25), aacA4 (n = 20), and blaCTX-M (n = 17) and carbapenemase genes were identified in nine specimens. Further studies are now required to determine the clinical impact of this new rapid test which could play a role in the successful treatment of IAI.

Claudin-1, miR-122 and apolipoprotein E transductions improve the permissivity of SNU-182, SNU-398 and SNU-449 hepatoma cells to hepatitis C virus.

Hepatitis C virus (HCV) is a human hepatotropic virus, but many hepatoma cell lines are not permissive to this virus. In a previous study, we observed that SNU-182, SNU-398 and SNU-449 hepatoma cell lines were nonpermissive to HCV. To understand the nonpermissivity, we evaluated the ability of each cell line to support the different steps of HCV life cycle (entry, replication and production of infectious particles). Using retroviral pseudoparticles pseudotyped with HCV envelope proteins and recombinant HCV produced in cell culture, we observed that low level or absence of claudin-1 (CLDN1) expression limited the viral entry process in SNU-182 and SNU-398 cells, respectively. Our results also showed that supplementation of the three cell lines with miR-122 partly restored the replication of a JFH1 HCV replicon. Finally, we observed that expression of apolipoprotein E (ApoE) was very low or undetectable in the three cell lines and that its ectopic expression permits the production of infectious viral particles in SNU-182 and SNU-398 cells but not in SNU-449 cells. Nevertheless, the supplementation of SNU-182, SNU-398 and SNU-449 cells with CLDN1, miR-122 and ApoE was not sufficient to render these cells as permissive as HuH-7 cells. Thus, these cell lines could serve as cell culture models for functional studies on the role of CLDN1, miR-122 and ApoE in HCV life cycle but also for the identification of new restriction and/or dependency host factors essential for HCV infection.

Comparison of MALDI-ToF MS with the Rapidec Carba NP test for the detection of carbapenemase-producing Enterobacteriaceae.

Although carbapenemase-producing Enterobacteriaceae (CPE) have become a serious public health issue, their detection remains challenging. The aim of this study was to implement a test based on imipenem hydrolysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS), using 65 strains producing or not a carbapenemase. Then, we compared its performance to that of the Rapidec Carba NP test using 20 additional strains. The MS-based test effectively discriminated between CPE and other non-carbapenem-susceptible strains compared to the Rapidec Carba NP test (sensitivity 100% and 92%, specificity 94% and 92%, respectively). The MS-based test gave less difficulty in interpretation than the colorimetric Rapidec Carba NP test. MALDI-ToF gave a result in less than one hour and limited the use of expensive molecular assays. In conclusion, the hydrolysis test based on MALDI-ToF MS can detect clinically relevant CPE isolates in routine practice. This technology, also described to screen for carbapenem resistance in Pseudomonas aeruginosa and Acinetobacter baumannii complex strains, also seems to be interesting in routine practice for these pathogens.

Factors associated with delayed screening of contacts of tuberculosis cases in the Somme, France.

AIM: To analyze the factors associated with the time to initiating tuberculosis contact investigations in the Somme department, France. METHODS: All reported tuberculosis cases and all their contacts screened between 2007 and 2011 were retrospectively included. Univariate and multivariate analyses were conducted to determine the factors associated with a "system delay"≤1 month and a "contact delay"≤0 days. RESULTS: The mean time between the mandatory notification of a case of tuberculosis and the date set for the contact's screening (system delay) was 35.3 days and the average time between that date and when the contact was actually screened (contact delay) was 12.5 days. In multivariate analysis, a smear-positive sputum sample (OR: 3.68; 95% CI: 1.63-8.30) and a diagnosis at the university hospital (OR: 2.61; 95% CI: 1.14-5.96) were significantly associated with a system delay≤1 month. A smear-positive sputum sample (OR: 1.35; 95% CI: 1.08-1.69), male gender (OR: 1.21; 95% CI: 1.01-1.49), being born in a foreign country (OR: 1.31; 95% CI: 1.02-1.69), being a family member (OR: 1.37; 95% CI: 1.05-1.77), or being another type of close contact of the case (OR: 2.47; 95% CI: 1.81-3.36) were significantly associated with a contact delay≤0 days. CONCLUSION: System and contact delays were longer than recommended, and the factors associated with the lengthening of these delays need to be taken into account.

Place of diagnostic tools in the identification of Anaerobiospirillum succiniciproducens bacteraemia.

Anaerobiospirillum succiniciproducens is a rare but potentially lethal pathogen. We report a case of A. succiniciproducens bloodstream infection in a 55-year-old man hospitalized for pelvic trauma. The strain was identified by 16sRNA sequencing after several failures of identification by MALDI-TOF MS. The strain was susceptible to beta-lactam antibiotics and ciprofloxacin, but resistant to macrolides and clindamycin. Identification tools must be improved to enhance our knowledge on this rare pathogen and to define optimal therapy.

Factors associated with time to mandatory tuberculosis notification in the Somme department, France.

BACKGROUND: The associated factors contributing to a delay in mandatory tuberculosis notification in the Somme department, France, are not yet known. The objective of this study was to analyze these factors. METHODS: All reported cases of tuberculosis between 2007 and 2011 were retrospectively included. Univariate and multivariate analyses were conducted to investigate the factors associated with a short time to notification, i.e., ≤48h. RESULTS: Between 2007 and 2011, a total of 175 cases of tuberculosis were reported to the Somme Regional Health Agency. Of the 145 (83.8%) cases of tuberculosis with at least one pulmonary location, 57.7% had a positive sputum smear. The mean time between the diagnosis of tuberculosis and mandatory notification was 6.1 days. It was 2.6 days for tuberculosis cases with a positive sputum smear versus 8.3 days for cases with a negative sputum smear; 2.0 days for severe cases and 6.3 days for simpler forms. In multivariate analysis, only a positive sputum smear was significantly associated with a short time to mandatory notification (OR 2.44; 95%CI 1.18-5.00; P=0.02). CONCLUSION: The time to mandatory notification is longer than recommended. Better collaboration between the parties involved in tuberculosis control and their continuing medical education could reduce this delay in the Somme department.

Are trans-complementation systems suitable for hepatitis C virus life cycle studies?

Complementation is a naturally occurring genetic mechanism that has been studied for a number of plus-strand RNA viruses. Although trans-complementation is well documented for Flaviviridae family viruses, the first such system for hepatitis C virus (HCV) was only described in 2005. Since then, the development of a number of HCV trans-complementation models has improved our knowledge of HCV protein functions and interactions, genome replication and viral particle assembly. These models have also been used to produce defective viruses and so improvements are necessary for vaccine assays. This review provides an update on HCV trans-complementation systems, the viral mechanisms studied therewith and the production and characterization of trans-encapsidated particles.

Strong correlation between liver and serum levels of hepatitis C virus core antigen and RNA in chronically infected patients.

HCV core antigen (Ag) and HCV RNA levels were evaluated in matched liver biopsy samples and sera from 22 patients with hepatitis C infection by using the quantitative Architect HCV Ag immunoassay and a real-time RT-qPCR assay, respectively. The data showed a strong correlation between liver and serum compartments of HCV Ag levels (r = 0.80) and HCV RNA levels (r = 0.87). In summary, the serum HCV Ag and RNA levels reflect the intrahepatic values.

Genetic recombination of the hepatitis C virus: clinical implications.

Genetic recombination is a well-known feature of RNA viruses that plays a significant role in their evolution. Although recombination is well documented for Flaviviridae family viruses, the first natural recombinant strain of hepatitis C virus (HCV) was identified as recently as 2002. Since then, a few other natural inter-genotypic, intra-genotypic and intra-subtype recombinant HCV strains have been described. However, the frequency of recombination may have been underestimated because not all known HCV recombinants are screened for in routine practice. Furthermore, the choice of treatment regimen and its predictive outcome remain problematic as the therapeutic strategy for HCV infection is genotype dependent. HCV recombination also raises many questions concerning its mechanisms and effects on the epidemiological and physiopathological features of the virus. This review provides an update on recombinant HCV strains, the process that gives rise to recombinants and clinical implications of recombination.

Molecular characterization of glycopeptide-resistant enterococci from hospitals of the picardy region (france).

We studied 138 glycopeptide-resistant enterococci (GRE) strains, consisting of 131 glycopeptide-resistant Enterococcus faecium (GREfm) and 7 glycopeptide-resistant Enterococcus faecalis (GREfs). The GREfm strains were resistant to penicillin, ampicillin, vancomycin, and teicoplanin, while the GREfs strains were only resistant to vancomycin and teicoplanin. The van A gene was the only glycopeptide determinant present in all GRE isolates investigated. Genes coding for Hyl and Hyl+ Esp were detected in 39 (29.8%) and 92 (70.2%) of the 131 GREfm isolates, respectively. Three of the 7 GREfs were positive for gelE+asa 1 genes, 3 for gel E gene, and 1 for asa 1 gene. The genetic relationship between the 138 GRE was analyzed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). GREfm isolates were clustered in a single genogroup (pulsotype A), and GREfs were clustered in six genogroups (pulsotypes B-G). Among the isolates investigated by MLST, only 18 PCR products were sequenced (12 E. faecium and 6 E. faecalis), and 9 sequence types (STs) were identified.

A 2-log drop in viral load at 1 month is the best predictor of sustained response in HCV patients with normal ALT: a kinetic prospective study.

The most reliable predictor of a sustained virological response in patients with persistently normal ALT has not been identified. We analysed 17 patients with genotype 1 chronic HCV who underwent therapy with pegylated interferon alfa 2b and ribavirin for 48 weeks. Two patients discontinued therapy within 28 days because of side effects and the remaining 15 patients were analysed in detail. An analysis of on treatment virological response using area under the receiver operating characteristic analyses showed that a 2 log drop in HCV RNA at day 28 was the best predictor of a sustained virological response and a failure to reduce viral load by 2 logs correctly identified patients with a low (<15%) probability of achieving a sustained virological response. Introduction of this early discontinuation rule in patients with normal ALT would allow nearly half of the patients to discontinue futile therapy at an early stage.

Prevalence of HPV genotypes determined by PCR and DNA sequencing in cervical specimens from French women with or without abnormalities.

BACKGROUND: Epidemiological data on human papillomavirus (HPV) are needed to estimate potential changes in type distribution induced by recent HPV vaccination strategies. OBJECTIVES AND STUDY DESIGN: The epidemiological distribution of HPV in 669 cervical specimens from French women with and without cytological abnormalities was evaluated using type-specific PCR or sequencing. The results were compared with those obtained using the Digene high-risk Hybrid Capture 2 (HR-HC2) assay. RESULTS: The overall prevalence of HPV was high (45.3%) in our study population. 285 of the 291 HPV-positive samples were typed. The distribution frequency concerned 34 different genotypes, with HPV16 being the most prevalent (32.6%). Other genotypes present were HPV31 (7.4%), HPV18, HPV 52 (both 6.0%), HPV6 (5.3%) and HPV66 (4.2%). The respective frequencies of all other genotypes were below 4%. The agreement with HR-HC2 was 78.8%. The distribution frequency data were also analyzed relatively to cytological and histological results. Our method enables the diagnosis of HPV infections with the additional advantage of genotyping. CONCLUSION: HPV infections in the area of France studied here involve numerous HPV types, but the high cumulative prevalences of types 16, 18, 6 and 11 (44.6% in total) would suggest a major impact of vaccination on these genotypes.

Hepatitis C Virus p7 membrane protein quasispecies variability in chronically infected patients treated with interferon and ribavirin, with or without amantadine.

A clinical study was carried out to compare the response rate of two groups of non-responder (NR) hepatitis C virus (HCV) genotype 1 chronically infected patients treated with interferon and ribavirin, with or without amantadine. The viral load decreased more markedly in the group treated by tritherapy including amantadine, but the response rate at the end of treatment was not significantly different between bitherapy and tritherapy. As amantadine could have an antiviral effect on the ion channel activity of the p7 HCV protein, the p7 quasispecies was characterized by cloning and sequencing. Sequence data were analyzed to determine the pattern and significance of p7 genetic heterogeneity and a possible relationship with therapy. Subtype differences were confirmed between p7 HCV genotypes 1a and 1b, and quasispecies analysis showed a reduction of genetic diversity in subtype 1a, but not 1b, during tritherapy. However, the absence of changes at numerous positions, as well as the conservative changes at other positions, indicated the high conservation of the p7 structure. Residue His-17, proposed to interact with amantadine, was fully conserved in both subtypes 1a and 1b, independently of amantadine administration. In conclusion, although the analysis of the p7 sequences revealed a selective pressure during therapy, no specific residues appeared to be linked to the effect of amantadine on viral decline. These results suggest that the potential antiviral effect of amantadine might be non-specific and related to a reduction in endosomal acidification and therefore reduced viral entry of HCV via its pH-dependent pathway.

Molecular diversity of Proteus mirabilis isolates producing extended-spectrum beta-lactamases in a French university hospital.

Between February 1997 and December 2002, 3340 hospitalised patients yielded samples positive for Proteus mirabilis, of whom 45 (1.3%) were colonised/infected by P. mirabilis producing extended-spectrum beta-lactamases (ESBLs). The gross incidence of patients colonised/infected by ESBL-producing P. mirabilis was 1.61/10(5) days of hospitalisation, with 20% of isolates being collected from patients in urology wards, most frequently (53.3%) from urine samples. Seventeen (37.7%) of the 43 isolates were obtained from samples collected within 48 h of hospitalisation, indicating that they were community-acquired. Isoelectric focusing assays and sequencing identified the TEM-24, TEM-92 and TEM-52 ESBLs. Pulsed-field gel electrophoresis revealed eight pulsotypes (I-VIII), with the two most common pulsotypes, IV and VI, comprising ten (23.3%) and 12 (26.6%) isolates, respectively. These pulsotypes were considered to represent epidemic strains and spread in various wards of the hospital.

Epidemiological and quantitative study of GBV-C infection in french polytransfused children.

From 1999 to 2002, 246 serum samples taken from polytransfused children were tested for the presence of GB virus C (GBV-C) RNA using a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. This assay was based on the TaqMan technology and allowed viral load determination in infected children with a dynamic range from 10(3) to 10(7) genome equivalent (gEq) copies/ml. The limit of detection was estimated to 619 gEq copies/ml with a > or = 95% probability of a positive result. Thirty five sera were found to be GBV-C RNA positive, corresponding to a prevalence of GBV-C of 14.2%. The mean viral load was high, i.e., 6 +/- 1.4 log (range 3.22-7.42) gEq copies/ml, but low viral loads were also detected. Sequencing of the 5'-untranslated region (UTR) identified a majority of genotype 2 strains (82%) distributed into two subtypes, 88.5% genotype 2a and 11.5% genotype 2b. In conclusion, GBV-C active infection is very frequent in exposed populations such as polytransfused children. GBV-C RNA quantitation using real-time assay may be useful for diagnosis and follow-up of the natural history of GBV-C infection.

Positive effect of the hepatitis C virus nonstructural 5A protein on viral multiplication.

Hepatitis C virus infection (HCV), is a major cause of liver disease worldwide, and are frequently resistant to the interferon alpha treatment. The nonstructural (NS) 5A protein of HCV has been proposed to be involved in this resistance. Additional studies have pointed out a role for NS5A in several other cellular interactions as well as an important role of its adaptative mutations in HCV genome replication. However, no infectious system is available to assess the role of NS5A in the HCV life cycle. Thus, we have constructed a recombinant system directly demonstrating for the first time that the expression of NS5A confers a multiplicative advantage to Sindbis virus, a virus close to HCV. This advantage seemed to be related to an anti-apoptotic effect of the NS5A protein. At a later stage, a possible nuclear localization of NS5A was observed, likely due to apoptotic cleavages of this protein. The NS5A protein was also shown to induce the interleukin-8 (IL-8) mRNA and to activate the NF-kappaB pathway independently of the Sindbis virus. Together, our data suggest that the activation of NF-kappaB could lead to the anti-apoptotic activity of NS5A and explain the viral multiplicative advantage conferred by the expression of the NS5A protein.