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Objectives: To describe the real-life use of temocillin for non-urinary tract infections, to assess its effectiveness in infections caused by ESBL-producing Enterobacterales, and to identify risk factors for treatment failure., Method: Retrospective multicentric study in 14 tertiary care hospitals, including all patients who received at least one dose of temocillin for ESBL infections from 1 January 2016 to 31 December 2021 for non-urinary tract infections. Failure was a composite criterion defined within 28 day follow-up by persistence or reappearance of signs of infection, and/or switch to suppressive antibiotic treatment and/or death from infection. Logistic regression with univariable and multivariable analysis was performed to identify risks associated with failure., Results: Data on 163 infection episodes were collected; 133 were due to ESBL-producing Enterobacterales and 128 were included in the effectiveness analysis. Median (IQR) age was 61 (53-70) years and 61.7% of patients were male. Main indications were lower respiratory tract infection (LRTI; 28.9%), intra-abdominal infections (IAI; 28.1%) and cutaneous infections (12.5%). The main bacteria involved were Klebsiella pneumoniae (48.4%), Escherichia coli (25.0%) and Enterobacter cloacae (24.2%). Polymicrobial infections occurred in 45.3% of cases. Temocillin was used as monotherapy in 86/128 (67.2%). Failure was found in 36/128 (28.1%) cases. In multivariable analysis, the only factor associated with failure was initial severity of the episode [adjusted OR 3.0 (95% CI: 1.06-8.69)]., Conclusions: During non-urinary tract infections, the main use of temocillin was for LRTIs and IAIs due to ESBL-producing E. coli and K. pneumoniae . The main risk factor for failure was initial severity of the disease., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Background: Oligella is an uncommon Gram-negative coccobacillus that was first thought to belong to the urogenital tract. The genus Oligella comprises two species that were recovered from various samples worldwide., Methods: We perform a systematic review focusing on Oligella microbiological characteristics, habitat, role in Human microbiome and infection, and antimicrobial susceptibility., Results: In humans, Oligella is mainly found as part of the microbiome of individuals with predisposing conditions. Oligella were also associated with invasive infections in patients with underlying diseases. Nevertheless, their prevalence remains to determine. Oligella culture requires up to 48 h on agar media in vitro, while urinary samples are usually incubated for 24 h. Consequently, microbiologists should be prompt to prolong the incubation of agar media when the direct examination showed Gram-negative coccobacilli. Oligella is accurately identified using MALDI-TOF mass spectrometry, but biochemical methods often provided inconsistent results. Specific guidelines for antimicrobial susceptibility testing of Oligella lack but the incubation could require up to 48 h of incubation. In contrast to O. urethralis, which is susceptible to third-generation cephalosporin, O. ureolytica is likely resistant to numerous antimicrobials. Genectic determinants of resistance were identified for beta-lactams and aminoglycosides., Conclusion: Oligella is an uncommon pathogen that can be underrecognized. Microbiologists should be prompt to prolong the incubation of agar media plated with urines when the direct examination showed Gram-negative coccobacilli. Carbapenems should probably be given for the empirical treatment., (© 2024. The Author(s).)

The combination of ceftazidime-avibactam (CAZ-AVI) and aztreonam (ATM) is used to treat MBL-producing Enterobacterales-related infections. The new combination aztreonam-avibactam (AZA) is currently in development. We compared results obtained with the new MIC test strip (MTS) AZA (Liofilchem) with broth microdilution method (BMD) on 41 MBL-producing Enterobacterales from 41 clinical samples. The MTS AZA was also compared to combination testing method using CAZ-AVI and ATM strips. Compared to BMD, categorical agreement (CA) was 100%. Compared with combination testing method, CA was 97.6%. The MTS AZA can be used to determine MICs levels of AZA or CAZ-AVI/ATM combinations., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

We assess the performances of the Alinity M STI assay (Abbott Molecular) in comparison to the Xpert CT/NG assay (Cepheid). We first retrospectively used a collection of 70 frozen samples of which 33, 31, and 6 were positives for Chlamydia trachomatis (CT), Neisseria gonorrhoea (NG), and both micro-organisms respectively. The Alinity M STI and the Xpert CT/NG results were in accordance for all. The mean difference in cycle threshold values between the Xpert CT/NG and the Alinity M STI were -1.6 and 0.0 for CT and NG respectively. Then 214 fresh samples collected from 121 patients were prospectively tested with both instruments. Anal swabs, throat swabs, vaginal swabs, and urines accounted each for about 25%. Seven (3.2%) samples of which 5 anal swabs, provided inconclusive results with the Alinity M STI. In conclusion, the Alinity M STI is an accurate device for the microbiological diagnosis of NG and CT infections., Competing Interests: Declaration of competing interest The authors declare there are no competing interests., (Copyright © 2024. Published by Elsevier Inc.)

Background: Urogenital Mollicutes, that is, Mycoplasma hominis and Ureaplasma spp., can colonize the urogenital tract. While urogenital colonization is frequent, infections are rare but should not be missed. Furthermore, extragenital infections are even rarer. Over the past years, they have been increasingly documented as a cause of hyperammonemia syndrome (HS) and post-surgical infections. We review the literature on studies focused on post-surgical infections and HS involving urogenital Mollicutes after thoracic surgery including lung (LTR) and heart (HTR) transplantation., Methods: A systematic review was performed by searching PubMed/Medline case reports, case series, cohort studies, and clinical trials. Cases of infections and HS by urogenital Mollicutes after HTR and LTR transplantations were reported., Results: Overall, urogenital Mollicutes were associated with 15 HS, 31 infections in HTR and LTR, and 18 post-thoracic surgical infections in another context. Post-surgical infections were reported in all contexts. They were mainly due to M hominis, the only species that could cultivate on standard enriched agar forming pinpoint colonies after 3-5 days of incubation. Microbiologists should be prompted to pinpoint colonies even if the examination of Gram-staining is negative. The patients' management required surgical treatment and antimicrobials, almost always tetracyclines and/or fluoroquinolones. Conversely, HS occurred almost exclusively in bilateral LTR and is more likely due to Ureaplasma spp. As Ureaplasma spp. do not cultivate on standard media, the microbiological diagnosis was performed using molecular methods., Conclusions: Infections involving urogenital Mollicute should be considered in LTR with HS. The overall rate of mortality is high and might be due in part to delay in etiologic diagnosis. Post-surgical infections were reported in all contexts. The route of contamination with Mollicutes remains unknown in HTR and non-transplant surgery, but evidence of transmission from donors has been documented for LTR., Competing Interests: Conflicts of interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Inc.)

Symptoms of COVID-19 are similar to the influenza virus, but because treatments and prognoses are different, it is important to accurately and rapidly differentiate these diseases. The aim of this study was to evaluate whether the analysis of complete blood count (CBC), including cellular population (CPD) data of leukocytes and automated flow cytometry analysis, could discriminate these pathologies. In total, 350 patients with COVID-19 and 102 patients with influenza were included between September 2021 and April 2022 in the tertiary hospital of Suresnes (France). Platelets were lower in patients with influenza than in patients with COVID-19, whereas the CD16 pos monocyte count and the ratio of the CD16 pos monocytes/total monocyte count were higher. Significant differences were observed for 9/56 CPD of COVID-19 and flu patients. A logistic regression model with 17 parameters, including among them 11 CPD, the haemoglobin level, the haematocrit, the red cell distribution width, and B-lymphocyte and CD16 pos monocyte levels, discriminates COVID-19 patients from flu patients. The sensitivity and efficiency of the model were 96.2 and 86.6%, respectively, with an area under the curve of 0.862. Classical parameters of CBC are very similar among the three infections, but CPD, CD16 pos monocytes, and B-lymphocyte levels can discriminate patients with COVID-19.

Background: To harmonize with the EUCAST breakpoints, the French Society of Microbiology introduced a change in the inhibition diameter breakpoint (17 mm versus 20 mm previously) of temocillin. We assessed the impact of the new breakpoints on categorizing susceptibility of Enterobacterales to temocillin., Methods: This was a multicentric retrospective study including all Enterobacterales isolates routinely tested for temocillin susceptibility with the disc diffusion method between 1 January 2016 and 31 July 2022 in four centres. Categorization using the breakpoints of 20 mm (French guidelines CA-SFM/EUCAST 2020 v.1.1) and 17 mm (French guidelines CA-SFM/EUCAST 2021 v1.0 and EUCAST guidelines v11.0) was performed., Results: Overall, 36 416 Enterobacterales isolates were included. The overall rate of temocillin resistance decreased from 11.3% to 4.7% (relative difference of 58.5%) when using the 17 mm breakpoint instead of the 20 mm breakpoint, respectively. The relative change ranged from -44.0% in Klebsiella aerogenes to -72.7% in Klebsiella oxytoca . The median inhibition diameter was 23 mm (IQR 21-25). The isolates with a diameter of 20 mm appeared overrepresented, whereas those with a diameter of 18 and 19 mm were underrepresented. We therefore reviewed the diameters between 18 and 21 mm of 273 isolates. Thirty-two (11.7%) of them categorized as susceptible at first measure were controlled resistant at second measure., Conclusions: The new breakpoint induced a decrease in the rate of isolates categorized as resistant to temocillin, increasing therapeutic choice including for Extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE). We suggest the bias in measuring the inhibition diameter is probably related to the fact that temocillin is considered remarkably stable against broad-spectrum β-lactamases., (© The Author(s) 2023. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Background: Although rapid screening for and diagnosis of coronavirus disease 2019 (COVID-19) are still urgently needed, most current testing methods are long, costly or poorly specific. The objective of the present study was to determine whether or not artificial-intelligence-enhanced real-time mass spectrometry breath analysis is a reliable, safe, rapid means of screening ambulatory patients for COVID-19., Methods: In two prospective, open, interventional studies in a single university hospital, we used real-time, proton transfer reaction time-of-flight mass spectrometry to perform a metabolomic analysis of exhaled breath from adults requiring screening for COVID-19. Artificial intelligence and machine learning techniques were used to build mathematical models based on breath analysis data either alone or combined with patient metadata., Results: We obtained breath samples from 173 participants, of whom 67 had proven COVID-19. After using machine learning algorithms to process breath analysis data and further enhancing the model using patient metadata, our method was able to differentiate between COVID-19-positive and -negative participants with a sensitivity of 98%, a specificity of 74%, a negative predictive value of 98%, a positive predictive value of 72% and an area under the receiver operating characteristic curve of 0.961. The predictive performance was similar for asymptomatic, weakly symptomatic and symptomatic participants and was not biased by COVID-19 vaccination status., Conclusions: Real-time, noninvasive, artificial-intelligence-enhanced mass spectrometry breath analysis might be a reliable, safe, rapid, cost-effective, high-throughput method for COVID-19 screening., Competing Interests: Conflict of interest: S. Grassin-Delyle and C. Roquencourt are named as inventors on a patent application covering breath analysis in COVID-19 (WO 2022/058796, A method for analysing a breath sample for screening, diagnosis or monitoring of SARS-CoV-2 carriage or infection (COVID-19) on humans). Conflict of interest: The remaining authors declare no other conflicts of interest., (Copyright ©The authors 2023.)

The COVID-19 pandemic has strongly impacted healthcare settings. We assess changes in blood culture practices and results during the COVID-19 era. All blood culture vials processed between January 1, 2017, and December 31, 2020, by 3 clinical laboratories were included. A baseline period from January 1, 2017 to December 31, 2019, was compared to the year 2020. COVID-19 "waves" were defined as follows: "wave 1" from March 16 to May 10, 2020, and "wave 2" from October 29 to December 14, 2020. A mean of 143.5 and 158.6 vials per day were processed in 2019 and 2020 respectively. Up to 300 and 220 vials per day were processed during waves 1 and 2. Among positive vials, a higher rate of contaminant was noticed during wave 1 (55.9% vs 45.0%; P < 0.0001) and interwave (46.0% vs 38.6%; P < 0.0001) in comparison to previous years. The prevalence of contaminants returned to the baseline level during wave 2. Streptococcus pneumonia prevalence fell in 2020 in comparison to the baseline (0.4% vs 1.4%; P < 0.0001). The COVID-19 pandemic was associated with an increase in the number of blood culture vials processed, the rate of contaminants, and a fall in the number of pneumococcal bloodstream infections., Competing Interests: Declaration of Competing Interest The author have no competing interest to disclose., (Copyright © 2023 Elsevier Inc. All rights reserved.)

The respiratory tract of lung transplant recipients (LTR) is likely to be colonized with non-fermentative Gram-negative rods. As a consequence of the improvements in molecular sequencing and taxonomy, an increasing number of bacterial species have been described. We performed a review of the literature of bacterial infections in LTR involving non-fermentative Gram-negative rods with exclusion of Pseudomonas aeruginosa , Stenotrophomonas maltophilia , Achromobacter spp. and Burkholderia spp. Overall, non-fermenting GNR were recovered from 17 LTR involving the following genera: Acetobacter , Bordetella , Chryseobacterium , Elizabethkinga , Inquilinus , and Pandoraea . We then discuss the issues raised by these bacteria, including detection and identification, antimicrobial resistance, pathogenesis, and cross-transmission.

Objectives: Ceftolozane-tazobactam (C/T) proved its efficacy for the treatment of infections caused by non-carbapenemase producing Pseudomonas aeruginosa and Enterobacterales. Here, we aimed to provide susceptibility data on a large series of Enterobacterales since the revision of EUCAST categorization breakpoints in 2020., Methods: First, C/T susceptibility was determined on characterized Enterobacterales resistant to third generation cephalosporins (3GCs) (extended spectrum β-lactamase [ESBL] production or different levels of AmpC overexpression) (n = 213) and carbapenem-resistant Enterobacterales (CRE) (n = 259), including 170 carbapenemase producers (CPE). Then, 1632 consecutive clinical Enterobacterales responsible for infection were prospectively collected in 23 French hospitals. C/T susceptibility was determined by E-test® (biomérieux) and broth microdilution (BMD) (Sensititre™, Thermo Scientific) to perform method comparison., Results: Within the collection isolates, 88% of 3GC resistant strains were susceptible to C/T, with important variation depending on the resistance mechanism: 93% vs. 13% susceptibility for CTX-M and SHV-ESBL producers, respectively. Only 20% of the CRE were susceptible to C/T. Among CPE, 80% of OXA-48-like producers were susceptible to C/T, whereas all metallo-β-lactamase producers were resistant. The prospective study revealed that 95.6% of clinical isolates were susceptible to C/T. Method comparison performed on these 1632 clinical isolates demonstrated 99% of categorization agreement between MIC to C/T determined by E-test® in comparison with the BMD (reference) and only 74% of essential agreement., Conclusion: Overall, C/T showed good activity against wild-type Enterobacterales, AmpC producers, and ESBL-producing Escherichia coli but is less active against ESBL-producing Klebsiella pneumoniae, and CRE. E-test® led to an underestimation of the MICs in comparison to the BMD reference., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

SeptiCyte ® RAPID is a gene expression assay measuring the relative expression levels of host response genes PLA2G7 and PLAC8, indicative of a dysregulated immune response during sepsis. As severe forms of COVID-19 may be considered viral sepsis, we evaluated SeptiCyte RAPID in a series of 94 patients admitted to Foch Hospital (Suresnes, France) with proven SARS-CoV-2 infection. EDTA blood was collected in the emergency department (ED) in 67 cases, in the intensive care unit (ICU) in 23 cases and in conventional units in 4 cases. SeptiScore (0-15 scale) increased with COVID-19 severity. Patients in ICU had the highest SeptiScores, producing values comparable to 8 patients with culture-confirmed bacterial sepsis. Receiver operating characteristic (ROC) curve analysis had an area under the curve (AUC) of 0.81 for discriminating patients requiring ICU admission from patients who were immediately discharged or from patients requiring hospitalization in conventional units. SeptiScores increased with the extent of the lung injury. For 68 patients, a chest computed tomography (CT) scan was performed within 24 h of COVID-19 diagnosis. SeptiScore >7 suggested lung injury ≥50% (AUC = 0.86). SeptiCyte RAPID was compared to other biomarkers for discriminating Critical + Severe COVID-19 in ICU, versus Moderate + Mild COVID-19 not in ICU. The mean AUC for SeptiCyte RAPID was superior to that of any individual biomarker or combination thereof. In contrast to C-reactive protein (CRP), correlation of SeptiScore with lung injury was not impacted by treatment with anti-inflammatory agents. SeptiCyte RAPID can be a useful tool to identify patients with severe forms of COVID-19 in ED, as well as during follow-up.

Objectives: To describe two linezolid-resistant MRSA strains carrying the cfr(B) gene detected in the French National Reference Centre for staphylococci., Methods: Two linezolid-resistant MRSA strains isolated from cystic fibrosis patients in two different French hospitals in 2017 and 2019 were examined to explore the mechanisms of linezolid resistance. Antimicrobial susceptibility was tested using broth microdilution and gradient strips. The genetic determinants of linezolid resistance were assessed by a multiplex PCR targeting cfr/cfr(B), optrA and poxtA genes, by amplification and sequencing of individual 23S rRNA genes and by WGS using both Illumina and Nanopore technologies., Results: The two MRSA strains were resistant to linezolid but susceptible to tedizolid, and PCR-positive for cfr/cfr(B). The WGS analysis indicated that they belonged to two different STs (ST8-MRSA-IV and ST5382-MRSA-IV) and that they both harboured the cfr(B) gene on the same 9.7 kb Tn6218-like chromosomal transposon, a finding only previously reported in Enterococcus sp. and Clostridioides difficile., Conclusions: To the best of our knowledge, this is the first description of the presence of cfr(B) in staphylococci, more specifically in linezolid-resistant MRSA strains. This finding illustrates the risk of horizontal intergenus transfer of oxazolidinone resistance genes in Staphylococcus aureus and highlights the need to monitor such emergence in this species., (© The Author(s) 2022. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Human respiratory syncytial virus (RSV) is responsible of lower respiratory tract infections which may be severe in infants, elderly and immunocompromised adults. Europe and North-American countries have observed a massive reduction of RSV incidence during the 2020-2021 winter season. Using a systematic RSV detection coupled to SARS-CoV-2 for all adult patients admitted at the Foch hospital (Suresnes, France) between January and March 2021 (n = 11,324), only eight RSV infections in patients with prolonged RNA shedding were diagnosed. RSV whole-genome sequencing revealed that six and two patients were infected by RSV groups A and B, respectively. RSV carriage lasted from 7 to at least 30 days disregarding of RSV lineage. The most prolonged RSV shedding was observed in an asymptomatic patient. We detected novel patient-specific non-synonymous mutations in the G glycoprotein gene, including a double identical mutation in the repeated region for one patient. No additional mutation occurred in the RSV genome over the course of infection in the four patients tested for. In conclusion, our results suggest that the temporal shift in the RSV epidemic is not likely to be explained by the emergence of a high frequency, unreported variant. Moreover, prolonged RSV carriages in asymptomatic patients could play a role in virus spread., Competing Interests: Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier B.V.)

Aim: Meropenem-vaborbactam and delafloxacin activities were not assessed against Achromobacter spp. ( Achr ), Burkholderia cepacia complex ( Bcc ) and Stenotrophomonas maltophilia ( Smal ). Methodology: A total of 106 Achr , 57 Bcc  and 100 Smal  were tested with gradient diffusion test of meropenem-vaborbactam, delafloxacin and comparators. Results: Meropenem-vaborbactam MIC 50 were 4 μg/ml for Achr , 1 μg/ml for B. cepacia , 2 μg/ml for B. cenocepacia and B. multivorans , and 32 μg/ml for Smal . Delafloxacin MIC 50 were 4 μg/ml for Achr , 0.25 μg/ml for B. cepacia and B. multivorans , 2 μg/ml for B. cenocepacia , and 0.5 μg/m for Smal . meropenem-vaborbactam MICs were fourfold lower than meropenem for 28.3% Achr , 77.2% B. cepacia , 53.8% B. cenocepacia and 77.2% B. multivorans . Conclusion: Meropenem-vaborbactam and delafloxacin are in vitro active against Bcc and Achr .

Background and Aims: Beckman Coulter hematology analysers identify leukocytes by their volume (V), conductivity (C) and scatter (S) of a laser beam at different angles. Each leukocyte sub-population [neutrophils (NE), lymphocytes (LY), monocytes (MO)] is characterized by the mean (MN) and the standard deviation (SD) of 7 measurements called "cellular population data" (@CPD), corresponding to morphological analysis of the leukocytes. As severe forms of infections to SARS-CoV-2 are characterized by a functional activation of mononuclear cells, leading to a cytokine storm, we evaluated whether CPD variations are correlated to the inflammation state, oxygen requirement and lung damage and whether CPD analysis could be useful for a triage of patients with COVID-19 in the Emergency Department (ED) and could help to identify patients with a high risk of worsening., Materials and Method: The CPD of 825 consecutive patients with proven COVID-19 presenting to the ED were recorded and compared to classical biochemical parameters, the need for hospitalization in the ward or ICU, the need for oxygen, or lung injury on CT-scan., Results: 40 of the 42 CPD were significantly modified in COVID-19 patients in comparison to 245 controls. @MN-V-MO and @SD-V-MO were highly correlated with C-reactive protein, procalcitonin, ferritin and D-dimers. SD-UMALS-LY > 21.45 and > 23.92 identified, respectively, patients with critical lung injuries (>75%) and requiring tracheal intubation. @SD-V-MO > 25.03 and @SD-V-NE > 19.4 identified patients required immediate ICU admission, whereas a @MN-V-MO < 183 suggested that the patient could be immediately discharged. Using logistic regression, the combination of 8 CPD with platelet and basophil counts and the existence of diabetes or obesity could identify patients requiring ICU after a first stay in conventional wards (area under the curve = 0.843)., Conclusion: CPD analysis constitutes an easy and inexpensive tool for triage and prognosis of COVID-19 patients in the ED., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: D. Sukhachev is an employee of a Beckman Coulter distribution company in Russia, he performed the statistical analysis part; Elena Sukhacheva is director of medical and scientific affairs at Beckman-Coulter; we discussed about the interest of the study and checked that all that I had written about cellular population data was correct, (© 2023 The Authors.)

The Cycle Threshold (Ct) value of SARS-CoV-2 RT-PCR are used as an indicator of viral load. Using a collection of 45 fresh nasopharyngeal samples collected on universal transport media, we compare the Ct value obtained with 2 RT-PCR assays, the Alinity M SARS-CoV-2 and the Alinity M RESP-4-Plex (Abbott Molecular, Des Plaines, Illinois, Etats-Unis) processed on an Alinity M device. The assays are highly correlated; however, the Ct values were in median lower of 4.54 with the Alinity M RESP-4-Plex. This difference could be attributed to earlier detection of positivity by the software of the Alinity M rather than a difference in RT-PCR performances. The Ct-value of SARS-CoV-2 RT-PCR should be interpreted with caution taking into account the clinical context, pre-analytical and analytical findings.

Objectives: During bloodstream infections, reducing the time to antimicrobial susceptibility testing is crucial to initiation of early appropriate antibiotic therapy. For Gram-negative infections, a phenotypic approach remains necessary. Rapid antimicrobial testing (RAST) is a recently developed phenotypic EUCAST method. The goal of this study was to evaluate the accuracy and clinical impact of RAST., Patients and Methods: From September 2020 to August 2021, Gram-negative episodes with positive blood culture detected in the morning were included in the RAST group. Categorical agreement of RAST with conventional antimicrobial testing on strains was determined. To assess antibiotic management and patient outcomes, the RAST group was compared with a control group (CG) with positive blood culture detected in the afternoon for which overnight antimicrobial testing was performed., Results: The RAST group included 61 episodes from 61 patients, while the CG group included 49 episodes from 48 patients. While RAST performed on 41 E. coli, 11 K. pneumoniae and 9 P. aeruginosa strains highlighted 99.3 % of categorical agreement, 7.4 % of unreadable zones and 9.4 % of technical uncertainty area at 4 h incubation were also reported. For the RAST group, effective antibiotic therapy was prescribed in 100 % of patients on the day of positive blood culture (day 1) vs 88 % in CG (p = 0,007). As for beta-lactams on day 1, RAST led to 9 escalations and 6 de-escalations. Mortality and length of hospital stay did not significantly differ between the two groups., Conclusion: RAST improves management of antibiotic therapy in patients with Gram-negative sepsis., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Masson SAS. All rights reserved.)

Objectives: Asymptomatic sexually transmitted infections (STI) are frequent among men who have sex with men (MSM). Identifying asymptomatic STIs is a crucial issue, not only for secondary but also for primary prevention, as early treatment can reduce transmission risk. We aimed to develop a self-reported predictive score for early identification of asymptomatic STIs., Methods: Participants provided clinical data and completed a self-administered questionnaire including sociodemographic variables and behaviors during the 6 previous months. We used multivariable logistic regression to identify factors associated with asymptomatic STIs. We calculated the accuracy of the model by the non-parametric area (AUC) under the receiver-operating-characteristic (ROC) curve to find the optimal discriminant threshold for screening., Results: A total of 781 HIV-positive MSM were included with a mean age of 46.8 years. Asymptomatic STI prevalence was 13.2%. Detectable plasma HIV RNA (adjusted odds ratio (aOR [95% CI): 2.54 [1.23;5.25]), inconsistent condom use during anal sex (2.20 [1.36;3.56]), group sex (2.00 [1.15;3.45]), during or-genital practices (1.83 [1.12;3.01]), not being in stable relationship (1.70 [1.01;2.66] and an item from a sensation-seeking behavioral scale "I don't like watching porn videos" (1.61 [1.01;2.59] were associated with asymptomatic STI. AUC was 0.7 and with optimal threshold of 0.1082 for this model; sensitivity was 80.4%. Self-reported asymptomatic STI predictive score was built with this threshold according to the 6 factors in the final model., Conclusions: As this predictive score is not designed to be diagnostic, but to provide indications for diagnostic tests, its ease of administration and sensitivity remain the most important features. Its use in clinical practice for early detection of asymptomatic STIs potentially can reinforce STI primary and secondary prevention.

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a staple in clinical microbiology laboratories. Protein-profiling of bacteria using this technique has accelerated the identification of pathogens in diagnostic workflows. Recently, lipid profiling has emerged as a way to complement bacterial identification where protein-based methods fail to provide accurate results. This study aimed to address the challenge of rapid discrimination between Escherichia coli and Shigella spp. using MALDI-TOF MS in the negative ion mode for lipid profiling coupled with machine learning. Both E. coli and Shigella species are closely related; they share high sequence homology, reported for 16S rRNA gene sequence similarities between E. coli and Shigella spp. exceeding 99%, and a similar protein expression pattern but are epidemiologically distinct. A bacterial collection of 45 E. coli, 48 Shigella flexneri, and 62 Shigella sonnei clinical isolates were submitted to lipid profiling in negative ion mode using the MALDI Biotyper Sirius® system after treatment with mild-acid hydrolysis (acetic acid 1% v/v for 15 min at 98°C). Spectra were then analyzed using our in-house machine learning algorithm and top-ranked features used for the discrimination of the bacterial species. Here, as a proof-of-concept, we showed that lipid profiling might have the potential to differentiate E. coli from Shigella species using the analysis of the top five ranked features obtained by MALDI-TOF MS in the negative ion mode of the MALDI Biotyper Sirius® system. Based on this new approach, MALDI-TOF MS analysis of lipids might help pave the way toward these goals., (© 2022 The Authors. Microbiology Open published by John Wiley & Sons Ltd.)

Background: In the context of the SARS-CoV-2 pandemic, our interest was to evaluate the effect of COVID-19 during pregnancy on placenta and coagulation factors., Methods: a prospective cohort study between January and July 2021 of 55 pregnant women stratified into: Group O, 16 patients with ongoing SARS-CoV-2 infection at delivery; Group R, 21 patients with a history of SARS-CoV-2 infection during pregnancy but who recovered prior to delivery; Group C, 18 control patients with no infection at any time. All women had nasopharyngeal SARS-CoV-2 RT-PCR tests performed within 72 h of delivery. Obstetrical complications were recorded and two physiological inhibitors of coagulation, protein Z (PZ) and dependent protease inhibitor (ZPI), were analyzed in maternal and cord blood. All placentae were analyzed by a pathologist for vascular malperfusion., Results: No patient in any group had a severe COVID-19 infection. More obstetrical complications were observed in Group O (O: n = 6/16 (37%), R: n = 2/21 (10%), C: n = 1/18 (6%), p = 0.03). The incidence of placental vascular malperfusion was similar among the groups (O: n = 9/16 (56%), R: n = 8/21 (42%), C: n = 8/18 (44%), p = 0.68). No PZ or ZPI deficiency was associated with COVID-19. However, an increased ZPI/PZ ratio was observed in neonates of Group R (O: 82.6 (min 41.3-max 743.6), R: 120.7 (29.8-203.5), C: 66.8 (28.2-2043.5), p = 0.04)., Conclusion: COVID-19 was associated with more obstetrical complications, but not an increased incidence of placental lesions or PZ and ZPI abnormalities.

Background : The clinical presentation of viral respiratory infections is unspecific. We assessed the performances of two new RT-PCR, the Idylla™ SARS-CoV-2 and the Idylla™ SARS-CoV2/Flu/RSV, and two isothermal amplification assays, the ID NOW COVID and the ID NOW influenza A & B 2. Methods : The study was conducted in two parts: (i) the Idylla™ assays were assessed using a collection of nasopharyngeal swabs which were positive for various respiratory viruses. (ii) The performances of the four assays were assessed prospectively: all of the symptomatic patients admitted to the emergency department from 10 to 21 December were enrolled. Results: (i) All of the SARS-CoV-2 false negatives with the Idylla™ assays had a Ct value greater than 30 with the reference RT-PCR. No cross-reactivity was identified. (ii) Overall, 218 patients were enrolled. The respective prevalences of SARS-CoV-2, influenza A, and RSV were 19.8%, 4.8%, and 3.2%. All of the assays were 100% specific. The sensitivity of SARS-CoV-2 detection was 97.7%, 82.5%, and 86.3% for the Idylla™ SARS-CoV2, the Idylla™ SARS-CoV2/Flu/RSV, and the ID NOW COVID-19, respectively. For influenza A, it was 90.0% for the Idylla™ SARS-CoV2/Flu/RSV and 80.0% for the ID NOW Influenza. Discussion . All of the assays are suitable for testing patients with respiratory symptoms. False negatives should be considered, and the test should be repeated regarding the context.

Although Candida spp are aerobic microorganisms, some Candida strains, mainly Candida glabrata, can be recovered from anaerobic blood culture vials. We assessed the contribution of the anaerobic vials for the diagnosis of candidemia, especially for C. glabrata. We conducted a multicenter retrospective study including eight university or regional hospitals. A single episode of monomicrobial candidemia per patient was included from September 1st, 2016, to August 31st, 2019. The characteristics of all aerobic and anaerobic blood culture vials sampled within 2 h before and after the first positive blood culture vials were recorded (type of vials, result, and for positive vials time-to-positivity and Candida species). Overall, 509 episodes of candidemia were included. The main species were C. albicans (55.6%) followed by C. glabrata (17.1%), C. parapsilosis (4.9%), and C. tropicalis (4.5%). An anaerobic vial was positive in 76 (14.9%) of all episodes of which 56 (73.8%) were due to C. glabrata. The number of C. glabrata infections only positive in anaerobic vials was 1 (2.6%), 1 (11.1%), and 15 (37.5%) with the BACT/ALERT 3D the BACT/ALERT VIRTUO and the BACTEC FX instrument, respectively (P < 0.01). The initial positivity of an anaerobic vial was highly predictive of the isolation of C. glabrata with the BACTEC FX (sensitivity of 96.8%). C. glabrata time-to-positivity was shorter in anaerobic vial than aerobic vial with all instruments. Anaerobic blood culture vials improve the recovery of Candida spp mainly C. glabrata. This study could be completed by further analyses including mycological and pediatric vials., Lay Summary: Although Candida spp are aerobic microorganisms, C. glabrata is able to grow in anaerobic conditions. In blood culture, the time-to-positivity of C. glabrata is shorter in anaerobic than aerobic vials. Only the anaerobic vial was positive in up to 15 (37.5%) C. glabrata bloodstream infections., (© The Author(s) 2022. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

Zoonotic species of Capnocytophaga genus belong to the oral microbiota of dogs and cats. They may be responsible for serious human infections, mainly after animal bites, with a high mortality rate. In France, only few cases have been reported and no multicenter study has been conducted. Our aim was to describe the French epidemiology of Capnocytophaga zoonosis. We conducted a multicenter (21 centers) retrospective non-interventional, observational study in France describing the epidemiology of Capnocytophaga zoonosis (C. canimorsus, C. cynodegmi, C. canis) over 10 years with regard to clinical and bacteriological data. From 2009 to 2018, 44 cases of Capnocytophaga zoonotic infections were described (C. canimorsus, n = 41; C. cynodegmi, n = 3). We observed an increase (2.5 times) in the number of cases over the study period (from the first to the last 5 years of the study). The most frequent clinical presentations were sepsis (n = 37), skin and soft tissue infections (n = 12), meningitis (n = 8), osteoarticular infections (n = 6), and endocarditis (n = 2). About one-third of patients with sepsis went into septic shock. Mortality rate was 11%. Mortality and meningitis rates were significantly higher for alcoholic patients (p = 0.044 and p = 0.006, respectively). Other comorbidities included smoking, splenectomy, diabetes mellitus, and immunosuppressive therapy are associated to zoonotic Capnocytophaga infection. Eighty-two percent of cases involved contact with dogs, mostly included bites (63%). Despite all isolates were susceptible to the amoxicillin-clavulanic acid combination, three of them were resistant to amoxicillin., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

In the context of increasing antimicrobial resistance in Enterobacterales, the management of these UTIs has become challenging. We retrospectively assess the prevalence of antimicrobial resistance in Enterobacterales isolates recovered from urinary tract samples in France, between 1 September 2017, to 31 August 2018. Twenty-six French clinical laboratories provided the susceptibility of 134,162 Enterobacterales isolates to 17 antimicrobials. The most frequent species were E. coli (72.0%), Klebsiella pneumoniae (9.7%), Proteus mirabilis (5.8%), and Enterobacter cloacae complex (2.9%). The overall rate of ESBL-producing Enterobacterales was 6.7%, and ranged from 1.0% in P. mirabilis to 19.5% in K. pneumoniae , and from 3.1% in outpatients to 13.6% in long-term care facilities. Overall, 4.1%, 9.3% and 10.5% of the isolates were resistant to cefoxitin, temocillin and pivmecillinam. Cotrimoxazole was the less active compound with 23.4% resistance. Conversely, 4.4%, 12.9%, and 14.3% of the strains were resistant to fosfomycin, nitrofurantoin, and ciprofloxacin. However, less than 1% of E. coli was resistant to fosfomycin and nitrofurantoin. We identified several trends in antibiotics resistances among Enterobacterales isolates recovered from the urinary tract samples in France. Carbapenem-sparing drugs, such as temocillin, mecillinam, fosfomycin, cefoxitin, and nitrofurantoin, remained highly active, including towards ESBL-E.

Background: Rapid antigen detection assays are promising tools for the diagnosis of COVID-19. We assess the performances of the Panbio COVID-19 Ag Rapid Test., Methods: The Panbio COVID-19 Ag Rapid test was compared to a reference RT-PCR performed on the same nasopharyngeal swab (NPS). Overall, 81 NPS were tested retrospectively and 330 healthcare workers (HCWs) were tested prospectively., Results: Retrospective analyze. Of the 48 SARS-CoV-2 positive NPS, 19 (39.6%) were found positive with the Panbio COVID-19. There was no cross-reactivity with SARS-CoV-2 negative NPS. The Kappa value was 0.459. Prospective analyze. The prevalence of COVID-19 was 26.1% in symptomatic HCWs. The overall sensitivity and specificity of the Panbio COVID-19 were 47.2% and 100.0% respectively. The sensitivity was 55.2% and 14.3% in those tested within and after 4 days of diseases respectively., Conclusions: The Panbio COVID-19 Ag Rapid test displays low performance for the identification of SARS-CoV-2 infected patients.

Patients with viral respiratory infections often present symptoms compatible with bloodstream infections. Consequently, the winter period commonly associated with epidemic respiratory illnesses shows an increase in the number of blood cultures (BC) and to occasional saturation of automated BC systems. Here, we explored the seasonal variations in BC samples and the potential impact of shortening the incubation time of BC when automated BC systems are close to saturation. A retrospective study was conducted during a 3-year period in 4 hospitals located in the Paris region, France. All aerobic and anaerobic bottles were included, except pediatric bottles and those sampled for suspicion of endocarditis. The number of BC bottles collected during the winter period was compared to the annual baseline. All bottles positive after a 4-day incubation were analyzed regarding clinical and microbiological findings. The number of BC bottles was significantly higher during the winter periods, compared to the annual baseline (up to 14%). A total of 292,349 BC bottles were analyzed with 23,363 (8.0%) positive, including 236 (1%) after a 4-day incubation. Of these 236 bottles, 76 (64.8%) were positive with a contaminant, 78 (33.1%) with a clinically significant microorganism identified for the same patient in the previous 4 days, and only 5 (2.1%) with a clinically significant microorganism not previously identified. Winter periods were associated with a significant increase in BC samples. Shortening the incubation time of BC bottles from 5 to 4 days seems a relevant option when automated BC systems are close to saturation., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)