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The aim of this study was to investigate the relationship between nasal and rectal Staphylococcus aureus carriage in intensive care unit (ICU) patients and the occurrence of ICU-acquired infections related to S. aureus carriage. Three hundred and ninety-five patients admitted in ICU were screened for S. aureus nasal and rectal carriages and followed to record S. aureus infections during their stay. S. aureus strains were genotyped by arbitrarily primed PCR, spa-typing, microarray and whole genome sequencing. At ICU admission, 112 of 363 (30.9%) patients carried S. aureus including 61 (16.8%) exclusive nasal carriers, 40 (11.0%) combined nasal and rectal carriers and 11 (3.0%) exclusive rectal carriers. The 152 S. aureus isolates from nasal and rectal swabs belonged to 19 clonal complexes (CCs). Patients colonized in both nose and rectum harboured different strains in at least 40% of cases according to arbitrarily primed PCR data. Nasal carriers of CC5 S. aureus had an increased risk of rectal carriage (RR = 1.85, P

Highlights • In case of virus emergence, laboratory-developed assays (LDA) should be urgently assessed. • Recommended open one-step RT-qPCR reagents are rapidly on tension in case of pandemic. • Five other reagents were shown to be used for SARS-CoV-2 RNA detection by LDA. • This study can help laboratories to assess LDA for detecting emerging RNA viruses., Background Facing the emergence of a new RNA virus, clinical laboratories are often helpless in the face of a shortage of reagents recommended by Reference Centres. Objectives To compare five open one step RT-qPCR reagents to the SuperScript™ III Platinum™ One-Step qRT-PCR kit (Invitrogen) considered as the reference one in France at the beginning of the pandemic for detection of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in respiratory specimens by using laboratory-developed assay targeting the viral RNA dependant RNA polymerase (RdRp) gene. Study design A total of 51 NUCLISENS easyMAG extracts from respiratory specimens was tested on ABI 7500 thermocycler with TaqMan Fast Virus 1-Step Master Mix (Applied Biosystems), Luna® Universal Probe One-Step RT-qPCR Kit (New England Biolabs), GoTaq® Probe 1- Step RT-qPCR System (Promega), LightCycler® Multiplex RNA Virus Master (Roche) and One-step PrimeScript RT-PCR kit (Takara). The CT values obtained using the 5 challenged reagents were compared to those obtained using the reference assay. Results The percentages of concordance were all above 95 %. When comparing the CT values of the 48 extracts exhibiting CT values < 35 obtained with the reference reagent, the results were similar between the reagents although the differences of CT values were quite dispersed. Conclusions All five reagents can be considered as alternative reagents to the reference for detecting SARS−COV-2 RNA.

International audience; Meningococcal meningitis remains a life-threatening disease worldwide, with high prevalence in the sub-Saharan meningitis belt. A rapid diagnosis is crucial for implementing adapted antimicrobial treatment. We describe the performances of a new immunochromatographic test (MeningoSpeed, BioSpeedia, France) for detecting and grouping Neisseria meningitidis. Cerebrospinal fluids (CSFs) were collected from 5 African countries and France. For the rapid diagnostic test (RDT), the CSF sample was deposited on each of the 3 cassettes for a total volume of 90 μl. The results of the RDT were compared to those of a reference multiplex PCR assay detecting the major serogroups of N. meningitidis on 560 CSF specimens. Five specimens were found uninterpretable by RDT (0.9%). The results of interpretable specimens were as follows: 305 positive and 212 negative samples by both techniques, 14 positive by PCR only, and 24 positive by RDT only (sensitivity, specificity, and positive and negative predictive values of 92.7%, 93.8%, 95.6%, and 89.8%, respectively, with an accuracy of 93.2% and a kappa test of 0.89; P < 0.05). From 319 samples positive by PCR for serogroups A, C, W, X, or Y, the grouping results were concordant for 299 specimens (sensitivity of 93.0%, 74.4%, 98.1%, 100%, and 83.3% for serogroups A, C, W, X, and Y, respectively). The MeningoSpeed RDT exhibited excellent performances for the rapid detection of N. meningitidis antigens. It can be stored at room temperature, requires a minimal amount of CSF, is performed in 15 minutes or less, and is easy to use at bedside.

Objective Staphylococcus aureus dominates the skin microbiota in patients with atopic dermatitis (AD), with bacterial loads correlating with disease severity. The aim of this exploratory study was to investigate the effect of a cosmetic lotion containing heat-treated Lactobacillus johnsonii NCC 533 (HT La1) on S. aureus colonization in AD patients. Methods This open-label, multicenter study was performed in AD patients in Germany. First, detection of S. aureus was performed in all patients using the swab or scrub-wash method of sampling, followed by quantitative culture or quantitative polymerase chain reaction. Repeatability and reproducibility of all method combinations were evaluated to select the best combination of sampling and quantification. Second, a lotion containing HT La1 was applied to lesional skin twice daily for 3 weeks. Scoring using local objective SCORing Atopic Dermatitis (SCORAD), measurement of S. aureus load, and lesional microbiome analysis were performed before and after the 3-week treatment period. Results Thirty-one patients with AD were included in the study. All sampling and quantification methods were found to be robust, reproducible, and repeatable for assessing S. aureus load. For simplicity, a combination of swab and quantitative polymerase chain reaction was chosen to assess the efficacy of HT La1. Following application of a lotion containing HT La1 to AD lesions for 3 weeks, a reduction in S. aureus load was observed in patients, which correlated with a decrease in local objective SCORAD. Interestingly, high baseline skin concentrations of S. aureus were associated with good responses to the lotion. Conclusion This study demonstrated that the application of a lotion containing HT La1 to the lesional skin of patients with AD for 3 weeks controlled S. aureus colonization and was associated with local clinical improvement (SCORAD). These findings support further development of topical treatments containing heat-treated nonreplicating beneficial bacteria for patients with AD.

Worldwide, it is estimated that 140 million people suffer from shigellosis annually. The traditional identification of Shigella spp. by culture lacks sensitivity. Rapid diagnosis of shigellosis is important because it allows to engage appropriate antimicrobial treatment that shortens the duration and severity of the illness and reduces microbial carriage, thus the spread of infection in the community. Onestep immunochromatographic dipstick tests have been successfully developed at Institut Pasteur for Shigella spp., Shigella flexneri 2a, Shigella sonnei, and Shigella dysenteriae 1. The present work describes the evaluation of these four rapid diagnostic tests (RDT) that addressed the issue of rapid diagnosis of Shigella diarrhea and dysentery testing from bacterial cultures, stools, and rectal swabs which is usually how the specimen is often collected or received from the field or from remote settings. The evaluations have been performed in Chile, Democratic Republic of Congo, Senegal, Djibouti, Vietnam, India, and France, in dispensaries, in emergency room, on the field, in public health laboratories, and by the French Army. The dipstick method used requires minimal technical skill, and the test can be read between 5 and 15 minutes. Stool cultures and the immunochromatographic test showed concordant results in the comparative studies when RDT for S. sonnei was tested in Chile, Vietnam, India, and France; specificity (Sp) was 96% and sensitivity (Se) was 100%. When RDT for S. flexneri 2a was tested in Vietnam, Se was 91.5% and Sp was 99.2%. In Chile, Se was 83.3% and Sp was 100%. When RDT for S. dysenteriae 1 was tested in India, Vietnam, Senegal, and France by laboratory technicians and in Democratic Republic of Congo by a field technician, the Sp was 98.7% and the Se was 91.7%. In Chile, the initial finding for a simple RDT to diagnose Shigella spp. demonstrates its promising potential to become a powerful tool for case management and epidemiological surveys. Additionally, the dipsticks can be stored at room temperature in a humidity-proof plastic bag, making them easily transportable. Considering the potential impact these RDT have for the clinical management of the disease and for epidemiological studies, industrialization of these tests is in progress.

Rapid bacterial identification of positive blood culture is important for adapting the antimicrobial therapy in patients with blood stream infection. The aim of this study was to evaluate the performance of the multiplex FilmArray Blood Culture Identification (BCID) assay by comparison to an in-house protocol based on MALDI-TOF MS identification of microcolonies after a 4-hour culture, for identifying on the same day the microorganisms present in positive blood culture bottles. One hundred and fifty-three positive bottles from 123 patients were tested prospectively by the 3 techniques of bacterial identification: 11 bottles yielding negative results by the 3 tests were considered false positive (7.2%). The reference MALDI-TOF MS technique identified 134 monomicrobial (87.6%) and 8 double infections (5.2%), which resulted in a total of 150 microorganisms. Globally, 137 (91.3%) of these 150 pathogens were correctly identified by the fully automated multiplex FilmArray BCID system at the species or genus level on day of growth detection, versus 117 (78.8%) by MALDI-TOF MS identification on nascent microcolonies after a 4-hour culture (P < 0.01). By combining the two approaches, 140 (93.5%) of the positive bottles were identified successfully at day 0. These results confirm the excellent sensitivity of the FilmArray BCID assay, notably in case of multimicrobial infection. Due to the limited number of targets included into the test, it must be coupled to another identification strategy, as that presented in this study relying on MALDI-TOF MS identification of microcolonies obtained after a very short culture period.

Objective Staphylococcus aureus dominates the skin microbiota in patients with atopic dermatitis (AD), with bacterial loads correlating with disease severity. The aim of this exploratory study was to investigate the effect of a cosmetic lotion containing heat-treated Lactobacillus johnsonii NCC 533 (HT La1) on S. aureus colonization in AD patients. Methods This open-label, multicenter study was performed in AD patients in Germany. First, detection of S. aureus was performed in all patients using the swab or scrub-wash method of sampling, followed by quantitative culture or quantitative polymerase chain reaction. Repeatability and reproducibility of all method combinations were evaluated to select the best combination of sampling and quantification. Second, a lotion containing HT La1 was applied to lesional skin twice daily for 3 weeks. Scoring using local objective SCORing Atopic Dermatitis (SCORAD), measurement of S. aureus load, and lesional microbiome analysis were performed before and after the 3-week treatment period. Results Thirty-one patients with AD were included in the study. All sampling and quantification methods were found to be robust, reproducible, and repeatable for assessing S. aureus load. For simplicity, a combination of swab and quantitative polymerase chain reaction was chosen to assess the efficacy of HT La1. Following application of a lotion containing HT La1 to AD lesions for 3 weeks, a reduction in S. aureus load was observed in patients, which correlated with a decrease in local objective SCORAD. Interestingly, high baseline skin concentrations of S. aureus were associated with good responses to the lotion. Conclusion This study demonstrated that the application of a lotion containing HT La1 to the lesional skin of patients with AD for 3 weeks controlled S. aureus colonization and was associated with local clinical improvement (SCORAD). These findings support further development of topical treatments containing heat-treated nonreplicating beneficial bacteria for patients with AD.

During the 2012 Hajj season, the risk of acquisition of Staphylococcus aureus nasal carriage in a cohort of French pilgrims was 22.8%, and was statistically associated with the acquisition of viral respiratory pathogens (p 0.03). The carriage of S. aureus belonging to the emerging clonal complex 398 significantly increased following the pilgrimage (p

In contrast to Staphylococcus aureus intermittent nasal carriers, persistent ones have the highest risk of infection. This study reports the usefulness of a simple nasal sampling algorithm to identify the S. aureus nasal carriage state of hemodialysis patients (HPs) and their subsequent risk of infection. From a cohort of 85 HPs, 76 were screened for S. aureus nasal carriage once a week during a 10-week period. The S. aureus nasal load was quantified by using either culture on chromogenic medium or fully automated real-time polymerase chain reaction assay. Molecular typing was used to compare strains from carriage and infection. The algorithm based on quantitative cultures was able to determine the status of S. aureus nasal carriage with a sensitivity of 95.8%, a specificity of 94.2%, a positive predictive value of 88.5%, and a negative predictive value of 98.0%. Of note, the determination of the S. aureus carriage state was obtained on the first nasal sample for all the 76 HPs, but 1 (98.7%). The algorithm based on quantitative polymerase chain reaction assay directly from the specimen yielded similar performances. During the 1-year follow-up after the last sampling episode, HPs classified as persistent nasal carriers with the algorithm were found to have a higher risk of S. aureus infection than those classified as nonpersistent carriers (P