Culture remains the reference method for microbiological diagnosis of endophthalmitis, but its sensitivity is limited by small sample volumes, prior antibiotics, and fastidious organisms. This study evaluates the diagnostic contribution of 16S rRNA gene-targeted polymerase chain reaction (PCR) in improving bacterial identification in patients with endophthalmitis, compared to conventional culture. We conducted a retrospective cohort study including patients diagnosed with endophthalmitis and managed at Limoges University Hospital (France) from January 2018 to December 2024. Aqueous and/or vitreous samples were analyzed using both conventional culture and broad-range PCR targeting the bacterial 16S rRNA gene. The primary outcome was the global identification rate of pathogens by each method and their combination. Subgroup analyses considered the type of ocular sample. Seventy-one intraocular samples from 50 episodes were analyzed (41 aqueous humor, 30 vitreous). Culture allowed bacterial identification in 21.1

ABSTRACT Insertion sequences (IS) are widely involved in bacterial genomic plasticity by disrupting, adding, moving genomic sequences, or by activating or extinguishing gene expression. A specific family of IS, IS CR (for insertion sequence of Common Region), is thought to be involved in the dissemination of antibiotic resistance genes (ARGs). While some IS CR members are commonly found in bacteria isolated in clinical settings and can contribute to downstream ARG expression, the mechanisms regulating the IS CR -encoded transposase expression have remained uncharacterized. Here, we investigated the expression of the transposase genes of IS CR1 , IS CR2, and IS CR8 and its regulation in Escherichia coli . Using in silico analyses and in vitro experiments, we showed that the expression levels were extremely low, as observed for most IS transposases. We further demonstrated the direct role of DNA damages and the key SOS response repressor, LexA, in controlling the activity of the transposase promoter. These results provide evidence that the mobility of at least some IS CR elements may be promoted upon bacterial exposure to antibiotics inducing the SOS response. IMPORTANCE Mobile genetic elements (MGEs) are the most prevalent cause of antibiotic resistance emergence. Among these mobile elements, insertion sequences (IS) are well known to allow the dissemination of antibiotic resistance genes (ARGs) through the action of their transposase. Here, we studied the regulation of the transposase expression in a specific family of IS, the IS CR family, some members of which are known to be involved in antibiotic resistance. Characterizing the regulation of transposase expression is an important starting point for understanding how these IS can contribute, through their movement, to the spread and expression of antibiotic resistance.

Insertion sequences (IS) are key players in bacterial genome plasticity and horizontal gene transfer. IS91 family members, belonging to the HUH superfamily of single-strand nucleases, are often linked with antibiotic resistance genes. Among these, the element IS91 is unique as it also carries a sequence called orf121, whose stop codon overlaps with the start codon of tnpA, a highly conserved feature of IS91 isoforms. We show that Orf121 serves as a dual regulator of IS91 transposition: Orf121 inhibits transposition activity of TnpA while facilitating accurate excision of IS91 single-strand circular intermediates. This accurate excision reduces one-ended transposition events, i.e., events arising when proper termination fails, leading to the co-mobilization of adjacent DNA. We also provide evidence that the bottom-stranded ssDNA circular intermediate is the functional substrate IS91. These findings highlight a sophisticated regulatory strategy balancing IS91 mobility and genetic stability.

Background: Pseudomonas aeruginosa is a common pathogen involved in ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients. Our primary objective was to characterize and compare the genomes of consecutive P. aeruginosa respiratory isolates from one ICU using whole genome sequencing (WGS). Our secondary objective was to determine whether there is an association between P. aeruginosa virulence factors and VAP. Methods: In this retrospective observational monocentric study conducted over three years, we analyzed P. aeruginosa respiratory isolates from mechanically ventilated ICU patients. All consecutive isolates obtained from routine culturing were included. WGS was performed using the Ion GeneStudio (R) S5 platform. Bioinformatics analyses were executed using the PubMLST, ResFinder, and Virulence Finder databases. To identify potential genetic links among the isolates, single nucleotide polymorphisms (SNPs) were detected, and a phylogenetic tree was generated. The resistome results were compared to the antimicrobial susceptibility testing phenotypes following the EUCAST 2022 recommendations. The statistical association between virulence factors presence and VAP occurrence was evaluated using Fisher's exact test. Results: The 56 isolates collected from 47 patients showed high polyclonal diversity, with 32 different sequence types identified. The phylogenetic analysis revealed five clusters (with a low number of differing SNPs), putative clusters, and the presence of transmission clusters. Eight and nine isolates showed resistance to fluoroquinolones and ceftazidime, respectively. A positive association between exotoxin U (exoU) and VAP was evident (P = 0.051). Conclusion: Systematic WGS of P. aeruginosa respiratory isolates enabled the identification of clusters within one center. The exoU gene was positively (but non-significantly) associated with VAP.

In recent years, novel β-lactam-inhibitor combinations (imipenem-relebactam (I/R), meropenem-vaborbactam (M/V), aztreonam-avibactam (A/A)) have been commercialized and some are not yet on the market (cefepime-zidebactam (C/Z)). The objective of this study was to evaluate the efficacy of these β-lactam-β-lactamase inhibitors (BL/BLIs) combinations against a wide collection of French clinical multiresistant Enterobacterales isolates and to assess the performance of the E-test MIC method for I/R and M/V. BL/BLIs MICs were determined by broth microdilution on a collection of 200 ESBL-producing and 414 carbapenem-resistant clinical Enterobacterales (K. pneumoniae (271), E. coli (245), E. cloacae complex (48), other species (50)) including 292 carbapenemase-producing isolates. E-test method was evaluated for the determination of I/R and M/V MICs using 131 isolates from this collection. All the combinations were active against most ESBL-producing isolates (99-100 %), but C/Z and A/A MIC90 were lower than that of I/R and M/V (2mg/L and 2mg/L versus 8mg/L and 8mg/L). The M/V and I/R E-tests performances were close to those required by the FDA recommendations: Categorical agreement (CA) and Essential agreement (EA) ≥ 90 %, Major discrepancy (MD) and Very major discrepancy (VMD) < 3 %): 96.9 % (CA), 92.4 % (EA), 1.2 % (MD), 6.1 % (VMD) for I/R and 94.7 % (CA), 96.9 % (EA), 4.1 % (MD), 8.8 % (VMD) for M/V. This work confirmed the interest of C/Z and A/A combinations against carbapenem-resistant Enterobacterales isolates compared with M/V and I/R. Additionally, the findings indicate that the E-test method can be used for the determination of M/V and I/R MIC for E. coli and K. pneumoniae strains.

OBJECTIVES:This study evaluated the microbiological distribution and sensitivity of clinical strains from respiratory samples of inpatients to the antibiotics usually recommended for treatment of lower respiratory tract infection (LRTI). METHODS:Using the French SPARES (Surveillance et Prévention de l'AntibioRésistance en Etablissement de Santé) database, we recorded all respiratory microbiological samples collected in 2022 in 409 hospitals located in all regions of France. The distribution of main bacterial species and their resistance to the most frequently prescribed antibiotics for LRTI were compared by age group (18-64 years, 65-79 years, ≥ 80 years). RESULTS:Among 48,721 strains, 47.7 % were isolated from patients aged 18-64 years, 37.9 % aged 65-79 years, and 14.4 % aged ≥ 80 years. Enterobacteriaceae (30.1 %, 36.0 % and 35.1 %, respectively) and Pseudomonas aeruginosa (19.0 %, 25.0 % and 27.1 %) were the most prevalent pathogens, especially in older patients. Conversely, Haemophilus influenzae (14.5 %, 10.7 % and 8.7 %) and Streptococcus pneumoniae (8.3 %, 5.6 % and 3.4 %) were rare in older age. Overall antibiotic resistance increased with age across all classes: in increasing order of resistance, levofloxacin (9.2 %, 11.1 % and 13.2 %), piperacillin-tazobactam (14.5 %, 16.8 % and 17.4 %), cefotaxime (27.4 %, 34.3 % and 39.5 %), doxycycline (28.2 %, 37.4 % and 39.5 %), cotrimoxazole (32.1 %, 38.5 % and 40.2 %), and amoxicillin-clavulanate (37.2 %, 46.0 % and 51.4 %, p < 0.05 for all comparisons). More than half of the strains were resistant to amoxicillin and erythromycin. CONCLUSIONS:In this large nationwide database of respiratory samples, older age was associated with a high prevalence of Enterobacteriaceae and P. aeruginosa and beta-lactam resistance, a finding challenging current LRTI probabilistic treatment. Conversely, H. influenzae and S. pneumoniae were rarely observed in patients over 80 years of age.

Streptococcus pneumoniae infection is considered an uncommon cause of arthritis in adults. To determine the clinical and microbiological characteristics of pneumococcal septic arthritis, we retrospectively studied a large series of cases among adult patients during the 2010-2018 conjugate vaccine era in France. We identified 110 patients (56 women, 54 men; mean age 65 years), and cases included 82 native joint infections and 28 prosthetic joint infections. Most commonly affected were the knee (50/110) and hip (25/110). Concomitant pneumococcal infections were found in 37.2% (38/102) and bacteremia in 57.3% (55/96) of patients, and underlying conditions were noted for 81.4% (83/102). Mortality rate was 9.4% (8/85). The proportion of strains not susceptible to penicillin was 29.1% (32/110). Of the 55 serotyped strains, 31 (56.4%) were covered by standard pneumococcal vaccines; however, several nonvaccine serotypes (mainly 23B, 24F, and 15A) had emerged, for which susceptibility to β-lactams was low.

Antimicrobial resistance (AMR) causes over 35,000 deaths annually in the EU/EEA and is projected to result in 1.91 million global deaths each year by 2050. The second Joint Action on Antimicrobial Resistance and Healthcare-Associated Infections (EU-JAMRAI-2), uniting 128 partners from 30 countries, represents a coordinated EU/EEA effort to curb AMR through a One Health approach. Although nearly all EU/EEA countries have an AMR National Action Plan, our initial assessment revealed that implementation remains constrained by limited resources, weak intersectoral coordination and fragmented leadership. EU-JAMRAI-2 addresses these challenges by promoting harmonized surveillance, strengthening infection prevention and control, applying behaviorally tailored stewardship interventions, ensuring sustainable access to essential antibiotics, and raising awareness among priority target audiences. By analyzing policy gaps and operational barriers, this paper underscores the need for stronger accountability and political commitment to translate strategies into sustainable action. Strengthening AMR governance through a unified European approach is essential to achieve effective, lasting progress against this silent pandemic.

OBJECTIVES:Antimicrobial resistance (AMR) is a major public health concern worldwide. International travel is a risk factor for acquiring antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). Therefore, understanding the transmission of ARB and ARGs is instrumental in tackling AMR. This longitudinal study aimed to assess the benefit of wastewater monitoring in Guadeloupe to evaluate the role of tourism in the spread of AMR. METHODS:A wastewater-based surveillance (WBS) study was conducted to monitor AMR in Guadeloupe in 2022 during dry and wet seasons. We characterized the resistome, microbiome and exposome of water samples collected in wastewater treatment facilities of two cities with different levels of tourism activities, in the content of aircraft toilets, and the pumping station receiving effluents from hotels. RESULTS:The results show that the WBS approach facilitates the differentiation of various untreated effluents concerning exposome, microbiome, and resistome, offering insights into AMR dissemination. Additionally, the findings reveal that microbiome and exposome are comparable across sites and seasons, while resistome characterisation at specific locations may be pertinent for health surveillance. The microbiome of aircraft was predominantly composed of anaerobic bacteria from human intestinal microbiota, whereas the other locations exhibited a blend of human and environmental bacteria. Notably, individuals arriving by air have not introduced clinically significant resistance genes. Exposome compounds have been shown to influence the resistome's variance. CONCLUSIONS:Clear differences were seen between the aircraft and the local sampling sites, indicating that the contribution of tourism to the observed resistance in Guadeloupe is not significant.

We report discovery of a new bacterial genus and species of the family Pasteurellaceae by using phylogenetic and metabolic analysis. The bacterium, Emayella augustorita, was isolated from blood cultures of a patient in France diagnosed with an adenocarcinoma of the intestines and who was treated with a biliary prosthesis placement.

IntroductionPrésenter l'évolution entre 2009 et 2021 de la distribution des sérotypes et de la résistance aux béta-lactamines des souches de pneumocoque isolées d'infections invasives (IIP) chez l'adulte (>16 ans) et évaluer la place des vaccins PCV20 et PPV23.Matériels et méthodesEntre 2009, année précédant l'introduction du PCV13 en France, et 2021, 6055 souches isolées d'IIP chez l'adulte (1446 souches de liquide cérébro-spinal [LCS] et 4609 souches d'hémocultures [HEM]) ont été étudiées par les ORP pour leur sensibilité à l'amoxicilline (AMX) et au céfotaxime (CTX) en déterminant la CMI par microdilution en milieu liquide (interprétation selon le CA-SFM-EUCAST) et sérotypées par le Centre National de Référence du Pneumocoque.RésultatsEn 2021, les sérotypes du vaccin PCV13 ne représentaient plus que 23% des souches isolées de méningite et 25% de bactériémie versus 51% et 62% respectivement en 2009. Les sérotypes 3, 19A et 19F restaient encore très présents, ils représentaient 22% des souches. Parallèlement, on a noté une augmentation majeure du sérotype 8 qui représentait en 2021 8% des souches isolées de LCS et 20% d'HEM. Tous ces sérotypes sont compris dans le vaccin PPV23 et dans le PCV20. En 2021, le PPV23 couvrait 57% des sérotypes de méningites et 69% des sérotypes de bactériémies. Le vaccin PCV20 couvrait quant à lui 54% des sérotypes de méningites et 63% des sérotypes de bactériémies. A noter que le sérotype 9N, présent dans le PPV23 et absent du PCV20 représentait 5% des sérotypes impliqués dans les IIP chez l'adulte. Concernant les sérotypes non vaccinaux, les principaux (>3%) impliqués dans les IIP chez l'adulte en 2021 étaient le 15A (4%), 23A (3%), 23B (3%) et 24F (3%).En 2021, 6% des souches isolées d'HEM étaient résistantes à l'AMXiv (CMI >2mg/L), 12% à l'AMXpo (CMI >1mg/L) et 5 souches (0,5%) étaient résistantes au CTX (CMI >2mg/L). Concernant les souches isolées de LCS, 20% (n=23/115) avaient une CMI à l'AMX >0,5mg/L dont 7%, une CMI >2 mg/L. S'agissant du CTX, 17% (n=19/115) des souches avaient une CMI>0,5 mg/L. Parmi elles, 1 souche avait une CMI à 2 mg/L et 2 souches, une CMI de 4 mg/L.Les sérotypes les plus représentés étaient le 19F (27% des souches de CMI>0,5 mg/L pour AMX - 25% des souches de CMI>0,5 mg/L pour CTX), 19A (14% des souches de CMI>0,5 mg/L pour AMX - 12% des souches de CMI>0,5 mg/L pour CTX),le sérotype 11A (17% des souches de CMI>0,5 mg/L pour AMX - 17% des souches de CMI>0,5 mg/L pour CTX), le 15A (5% des souches de CMI>0,5 mg/L pour AMX - 10% des souches de CMI>0,5 mg/L pour CTX) et le 35B (12% des souches de CMI>0,5 mg/L pour AMX -12% des souches de CMI>0,5 mg/L pour CTX).ConclusionLes variations de la distribution des sérotypes dans le temps, l'augmentation croissante des résistances aux béta-lactamines dont les C3G ainsi que l'évolution des recommandations et des schémas vaccinaux soulignent l'importance de poursuivre la surveillance du pneumocoque afin d'adapter les futurs vaccins.Aucun lien d'intérêt

Septic patients with worst clinical prognosis have increased circulating immature granulocytes (IG), displaying limited phagocytosis and reactive oxygen species (ROS) production. Here, we developed an ex-vivo model of incubation of human granulocytes, from septic patients or healthy donors, with Escherichia coli. We showed that the ROS production in Sepsis-IG is lower due to decreased activation and protein expression of the NADPH oxidase complex. We also demonstrated that the low level of ROS production and lower phagocytosis of IG in sepsis induce the bacterial SOS response, leading to the expression of the SOS-regulated quinolone resistance gene qnrB2. Without antimicrobial pressure, the sepsis immune response alone may promote antibiotic resistance expression.

IntroductionEvaluer l'évolution entre 2009 et 2021 de la résistance aux bêta-lactamines et de la distribution des sérotypes dans les infections invasives pédiatriques à pneumocoque (IIPP).Matériels et méthodesEntre 2009, année précédant l'introduction du PCV13 en France, et 2021, les souches de pneumocoque isolées de liquide cérébro-spinal (LCS) et d'hémocultures (HEM) ont été collectés par les ORPs et étudiées pour leur résistance à l'amoxicilline (AMX) et au céfotaxime (CTX). Les sérotypes ont été réalisés au CNRP.RésultatsAu total, 1965 isolats de pneumocoque ont été collectés, 448 de LCS et 1517 HEM.S'agissant des isolats de LCS, leur nombre est passé de 106 en 2009 à 37 en 2021 (-65%). La stabilité observée entre 2015 et 2019 a été suivie par une nouvelle réduction en 2021 passant de 52 à 37 (-29%). Toutefois la proportion des méningites a augmenté parmi les IIPP passant de 18,4% en 2009 à 23,1 en 2021. La répartition des souches de méningites par tranche d'âges était la suivante : 0-23 mois 60%, 2-5 ans 17% et 6-15 ans 24%. En 2021, 30% des souches (n=11/37) avaient une CMI à l'AMX >0,5 mg/L dont 3 souches avec une CMI >2 mg/L et 16% des souches (n=6/37) avaient une CMI au CTX >0,5 mg/L dont 4 souches avec une CMI à 1 mg/L et 2 souches avec une CMI à 4 mg/L.S'agissant des isolats d'HEM, leur nombre est passé de 469 en 2009 à 123 en 2021 (-74%). La stabilité observée entre 2015 et 2017 a été suivie par une nouvelle réduction en 2021 passant de 154 à 123 (-20%). La répartition des souches d'HEM par tranche d'âges était la suivante : 0-23 mois 44%, 2-5 ans 36% et 6-15 ans 20%. En 2021, 16% des souches (n=20/123) avaient une CMI à l'AMX >0,5mg/L dont 12 souches avec une CMI >2 mg/L et 12% des souches (n=15/123) avaient une CMI au CTX >0,5 mg/L dont 9 souches avec une CMI à 1 mg/L et 6 souches avec une CMI à 2 mg/L.Le sérotype capsulaire a été déterminé pour 1821 souches. En 2009 les sérotypes du vaccin PCV13 représentaient 76% des IIPP et seulement 13% en 2021. S'agissant des vaccins PCV15 et PCV20, leurs sérotypes représentaient respectivement en 2009 78% et 85% des IIPP et en 2021 20% et 54% des IIPP. Les sérotypes les plus fréquents dans les IIPP en 2021 étaient les sérotypes non-vaccinaux 24F (16%), 10A (11%) et 15B/C (9%). Au sein des sérotypes non PCV13 émergents en 2021, 4/24 des souches 24F avaient une CMI AMX >0,5 mg/L et 8/10 des souches 11A avaient une CMI au CTX >0,5 mg/L.ConclusionLes variations de la distribution des sérotypes dans le temps soulignent l'importance de poursuivre la surveillance afin de dépister les évolutions dans la circulation des sérotypes, mais également de surveiller l'évolution de la résistance des souches aux antibiotiques. Cette surveillance est indispensable pour adapter la composition des futurs vaccins.Aucun lien d'intérêt

Antibiotic-resistance emergence and selection have become major public health issues globally. The presence of antibiotic resistant bacteria (ARB) in natural and anthroposophical environments threatens to compromise the sustainability of care in human and animal populations. This study was undertaken to develop a simple model formalizing the selective impact of antibiotics and pollutants on the dynamics of bacterial resistance in water and use the model to analyze longitudinal spatiotemporal data collected in hospital and urban wastewaters. Longitudinal-sampling data were collected between 2012 and 2015 in four different locations in Haute-Savoie, France: hospital and urban wastewaters, before and after water-treatment plants. Concentration in three different types of compounds: 1) heavy metals 2) antibiotics and 3) surfactants; and abundance of 88 individual genes and mobile genetic elements, mostly conferring resistance to antibiotics, were simultaneously collected. A simple hypothesis-driven model describing the weekly ARB dynamics was proposed to fit available data by assuming normalized gene abundance to be proportional to ARB populations in water. Compounds impacts on the dynamics of 17 genes found in multiple sites were estimated. We found that while mercury and vancomycin had relevant effects on ARB dynamics, respectively positively affecting the dynamics of 10 and 12 identified genes, surfactants antagonistically affected genes dynamics (identified for three genes). This simple model enables analyzing the relationship between resistance-gene persistence in aquatic environments and specific compounds inherent to human activities. Applying our model to longitudinal data, we identified compounds that act as co-selectors for antibiotic resistance. Highlights We analyzed longitudinal wastewater resistance genes and environmental data We developed a simple hypothesis-driven model to assess resistance selection Mercury and vancomycin were key drivers of antibiotic resistance in wastewater

Introduction Les maladies invasives à pneumocoques (IIP) restent une cause majeure de morbi-mortalité dans le monde. Malgré la diminution globale de la circulation des sérotypes du vaccin conjugué, la baisse de l'incidence de la maladie chez les adultes a été plus faible que prévu. En 2015, nous avons observé une augmentation de l'incidence des infections associées aux sérotypes 3 et 8 chez les adultes de plus de 65 ans. Cependant, grâce à cette évolution, les facteurs associés à la gravité de la maladie étaient peu connus. L'objectif de l'étude du groupe SIIPA était d'identifier les facteurs associés aux présentations sévères d'IIP, y compris les facteurs liés à l'hôte et aux sérotypes. Matériels et méthodes Nous avons mené une étude de cohorte prospective longitudinale, de 2014 à 2022, dans 25 centres français, incluant des patients adultes atteints d'IIP sans méningite (NCT03983616). Les données démographiques, cliniques et microbiologiques, y compris les sérotypes, ont été collectées prospectivement. Les cas graves ont été définis comme une septicémie sévère ou une admission en unité de soins intensifs. Les facteurs associés aux IIP graves ont été identifiés à l'aide d'une régression logistique avec un modèle polynomial fractionnaire multivariable. Résultats De 2014 à 2022, 1 931 cas de IIP ont été inclus ; 1 074 (56 %) étaient des hommes, 1 258 (65 %) étaient âgés de plus de 65 ans et 1 384/1 681 (82 %) étaient à risque d'IIP. Dans les 12 mois précédant l'IIP, 1 560/1 924 (81%) avaient consulté un praticien et 724/1 559 (46%) avaient été hospitalisés, tandis que 134/1 829 (7%) avaient été vaccinés contre le pneumocoque. Nous avons observé 913 (47%) cas sévères et 391 (20%) sont décédés pendant l'hospitalisation. Les patients à risque représentent 86,5 % des patients sévères (vs 78,5 % pour les patients non sévères, p<0,005). Chez les patients âgés de 65 ans et plus, le risque de développer une PI sévère est au moins 3 fois plus élevé que chez les patients plus jeunes (aOR 2,66, 95%CI [1,49-4,75], p=0,001). Les patients présentant des facteurs de risque ont un risque plus élevé de maladie pneumococcique grave, en particulier d'insuffisance cardiaque (1,56, 95%CI[1,19-2,04], p=0,001) et d'insuffisance rénale chronique (1,60, 95%CI[1,16-2,21], p=0,004). Les sérotypes 3 (1,91, 95 % IC [1,46-2,50], p<0,005), 19A (1,73, 95 % IC [1,13-2,67], p=0,012) et 19F (2,38, 95 % IC [1,25-4,54], p=0,008) étaient significativement associés à des IIP sévère. Conclusion Les facteurs liés à l'hôte et les sérotypes vaccinaux ont été associés à des formes sévères d'IIP. Si de nouveaux vaccins conjugués sont attendus en France en 2024, des efforts devraient être faits pour tenir compte de ces facteurs afin de préciser la cible des recommandations vaccinales et d'améliorer la couverture vaccinale dans les populations à risque.Liens d'intérêts déclarés :C.J. interventions ponctuelles, activité de conseil scientifique, invitation congrès par Pfizer et MSD

Background: Ventilator-associated pneumonia (VAP) is the main healthcare-associated infection in intensive care units with Staphylococcus aureus as the first pathogen in early VAP. Aim: To compare, using whole-genome sequencing (WGS), consecutive S. aureus isolates from lower respiratory samples of mechanically ventilated patients for identification of potential cross-transmissions; and to determine a potential link between S. aureus WGS data and patients with S. aureus early VAP. Methods: All mechanically ventilated patients with a documentation of respiratory S. aureus isolates were included over a two-year period. WGS allowed typing, comparative genomic and phylogenic analyses, as well as analyses of antibiotic resistance genes and virulence genes. Virulence genes were compared between patients who developed respiratory infectious event and those who did not. Findings: A total of 172 S. aureus isolates from 167 patients were sequenced. WGS revealed that the S. aureus population was polyclonal with only two potential healthcare cross-transmissions, each involving two isolates (2.3%). A very low resistance rate was observed with a strong genotypic/phenotypic association, and with a virulence profile highly dependent on the sequence type. No significant correlation was observed between VAP and virulence profile. Conclusion: This study on consecutive respiratory S. aureus isolates of mechanically ventilated patients revealed a very low level of cross-transmission. No association was observed between S. aureus WGS data and VAP occurrence. (c) 2024 The Authors. Published by Elsevier Ltd on behalf of The Healthcare Infection Society. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Background The increase in antibiotic resistance is a major public health issue. The development of rapid antimicrobial susceptibility testing (AST) methods is becoming a priority to ensure early and appropriate antibiotic therapy.Objectives To evaluate sedimentation field-flow fractionation (SdFFF) as a method for performing AST in less than 3 h.Methods SdFFF is based on the detection of early biophysical changes in bacteria, using a chromatographic-type technology. One hundred clinical Escherichia coli strains were studied. A calibrated bacterial suspension was incubated for 2 h at 37 degrees C in the absence (untreated) or presence (treated) of five antibiotics used at EUCAST breakpoint concentrations. Bacterial suspensions were then injected into the SdFFF machine. For each E. coli isolate, retention times and elution profiles of antibiotic-treated bacteria were compared with retention times and elution profiles of untreated bacteria. Algorithms comparing retention times and elution profiles were used to determine if the strain was susceptible or resistant. Performance evaluation was done according to CLSI and the ISO standard 20776-2:2021 with broth microdilution used as the reference method.Results AST results from SdFFF were obtained in less than 3 h. SdFFF showed high categorical agreement (99.8%), sensitivity (99.5%) and specificity (100.0%) with broth microdilution. Results for each antimicrobial were also in agreement with the ISO 20776-2 recommendations, with sensitivity and specificity of >= 95.0%.Conclusions This study showed that SdFFF can be used as a rapid, accurate and reliable phenotypic AST method with a turnaround time of less than 3 h.