SUMMARYInquilinus limosus is a nonfermentative Gram-negative rod that has been reported as an emergent pathogen, particularly in chronic respiratory diseases. I. limosus was first isolated from the airways of a lung transplant patient suffering from cystic fibrosis (CF). As I. limosus is almost exclusively recovered from the airways of CF patients, its identification may be challenging for non-CF specialists. Indeed, I. limosus is mainly isolated from the airways of CF patients, and its pathogenesis and treatments are still debated. We have extensively reported and reviewed the different clinical cases described in the literature, the identification methods used, and the antimicrobial susceptibility testing performed. Therefore, we provide here an exhaustive description of the phenotypic features and antimicrobial susceptibilities of I. limosus. Only seven I. limosus genomes are currently available in public databases. These genomes are not fully assembled and therefore allow only partial genomic analyses, which could not unveil antimicrobial resistance determinants or virulence factors. They are approximately 7 Mb in size and encode between 6,036 and 7,483 genes. Given that the available genomes are incomplete, our genomic analyses are still limited and would undoubtedly benefit from further fully sequenced and annotated genomes to provide additional information on the antibiotic resistance and pathogenesis of I. limosus. We anticipate that our review will be a starting point for more genome sequencing studies, as well as epidemiological studies, to provide additional information on I. limosus for better management of patients.

BACKGROUND:Infections due to AmpC-producing Enterobacterales represent an increasing therapeutic challenge. Third-generation cephalosporins may select resistant mutants, inducing clinicians to use cefepime or carbapenems and thereby contributing to carbapenem resistance. While temocillin is a narrow-spectrum beta-lactam stable against AmpC enzymes, evidence of its impact in non-urinary tract infections remains limited. METHODS:We conducted a retrospective study of adult patients treated with temocillin for non-urinary tract infections caused by AmpC-producing Enterobacterales between 2016 and 2021. Clinical, microbiological and therapeutic data were collected. The primary outcome was treatment failure within twenty-eight days. RESULTS:Six patients were included, with a median age of sixty-one years; three required intensive care. Infection sites were digestive or respiratory. All patients had achieved clinical cure by day twenty-eight, without recurrence, infection-related mortality, or adverse events. CONCLUSION:Having led to favorable outcomes, temocillin may represent a carbapenem-sparing option when in vitro susceptibility is confirmed. These findings call for further evaluation in larger prospective clinical studies.

OBJECTIVES:To characterize the intrinsic carbapenemase of Sphingobacterium spp. MATERIALS AND METHODS:Sphingobacterium spp. clinical isolates (n = 63) were collected in several French laboratories from 2012 to 2022. Antibiotic susceptibility was assessed by disc diffusion. MICs of last resort antimicrobials (including carbapenems, ceftazidime-avibactam, cefepime-enmetazobactam and cefiderocol) were determined by broth microdilution. WGS was performed on all isolates using the Illumina method. Cloning of the Sphingobacterium spiritivorum β-lactamase encoding gene, blaSPI-1, allowed expression of a novel metallo-β-lactamase (MBL), SPI-1, in Escherichia coli. Enzymatic kinetic parameters were determined with β-lactams as substrates. RESULTS:Among the 64 Sphingobacterium isolates collected we identified six species, of which S. spiritivorum (n = 24) was the most prevalent followed by S. multivorum (n = 20), S. siyangense (n = 16), S. lactis (n = 2), S. thalpophilum (n = 1) and S. faecium (n = 1). Sphingobacterium isolates displayed a phenotype of multidrug resistance including resistance to last resort β-lactams and β-lactam-β-lactamase inhibitors (with MIC50 at 4, 4 and 2 mg/L for ceftazidime-avibactam, cefepime-enmetazobactam and cefiderocol, respectively). The most effective drugs were fluoroquinolones, tigecycline and eravacycline. All S. spiritivorum displayed a carbapenemase activity that correlated with the identification of SPI-1 encoding genes. SPI-like variants (n = 10) shared 93.7% amino-acid identity, but only 50.6% identity with the closest CGB-1 MBL intrinsic of Chryseobacterium gleum. Characterization of SPI-1 showed a strong hydrolytic activity towards most β-lactams including carbapenems. CONCLUSION:S. spiritivorum was the most prevalent species of Sphingobacterium identified in clinical samples. All S. spiritivorum-like species produced a chromosomally encoded SPI-like MBL that might be challenging for the treatment of infections caused by this bacterial species.

INTRODUCTION:Recent attention to the role of the microbiome in oral cancer has prompted investigations into its potential contribution to oropharyngeal squamous cell carcinoma (OPSCC), given their anatomical and immunological overlap. However, consistent microbial patterns have not been identified across studies. METHODS:A systematic review, following PRISMA guidelines, examined studies on the role of the oral/oropharyngeal microbiome in OPSCC development, including its statistical relevance in cancer occurrence and prognosis. RESULTS:From 131 articles (2017-2025), 19 involving 4502 patients were analyzed. Increases in Porphyromonas gingivalis, Tannerella forsythia, and Fusobacterium were noted in OPSCC patients. However, no bacterial taxa were reproducibly identified across all studies, reflecting substantial heterogeneity and limited overlap. CONCLUSION:HPV, smoking, and cancer affect microbiota composition. The absence of reproducible microbial signatures highlights the need for more standardized, large-scale, and mechanistically driven studies to clarify the microbiome's role in OPSCC.

AIM:The aim of this study was to describe the bacterial epidemiology and antibiotic resistance rates of bacterial isolates collected from urine specimens in male patients with suspected urinary tract infection (UTI). METHODS:This retrospective multicenter study included routine data from midstream urine cultures of adult male patients with suspected UTI admitted to the emergency departments of 15 hospitals from 2019 to 2023. Urinalysis was performed according to the recommendations of the French Society for Microbiology and bacterial identification was carried out using MALDI-TOF mass spectrometry. Antimicrobial susceptibility testing was performed by disk diffusion or semi-automated methods and interpreted according to the CA-SFM/EUCAST guidelines. RESULTS:Overall, 38,279 bacterial isolates were detected among 33,113 male patients (mean age = 70.7 years). The most frequently encountered pathogen was E. coli (40.0 %) followed by E. faecalis (13.2 %), K. pneumoniae (7.8 %) and P. mirabilis (5.8 %). Overall prevalence of ESBL-E was 9.0 %, represented mainly by K. pneumoniae (22.8 %), E. cloacae complex (19.3 %) and E. coli (8.4 %). Prevalence of resistance to fluoroquinolones and cotrimoxazole was high (usually > 15-20 %). The resistance rates in E. coli were very low (around 1 %) for fosfomycin and nitrofurantoin, as was the overall prevalence of carbapenemase-producing Enterobacterales (0.1 %). In S. aureus, 20.4 % of isolates were resistant to methicillin, and only three vancomycin-resistant enterococci (<0.01 %) were detected. CONCLUSION:This original study provides recent, nationwide and helpful data on bacterial epidemiology and antibiotic resistance rates of isolates recovered from urines in male patients with suspected UTIs.

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. We perform a systematic review focusing on Oligella microbiological characteristics, habitat, role in Human microbiome and infection, and antimicrobial susceptibility. 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. 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.

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.

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. (c) Published by Elsevier Inc. on behalf of International Society for Heart and Lung Transplantation.

Background Human Metapneumovirus (HMPV) belongs to the Pneumoviridae family and is responsible for respiratory infections. Mild infections are well-recognized in children, while its precise impact in various categories of immunocompromised adults has not been well addressed. Research question We retrospectively studied HMPV infections in immunocompromised adults followed in two large French university medical centers. Study design and methods We identified immunocompromised adults with positive HMPV Polymerase Chain Reaction (PCR) for 36 months and reviewed their medical charts. For lung transplant recipients (LTR), FEV1 was collected at baseline, during and after infection. Imaging was centralized and chest involvement was categorized by dominant CT patterns. We compared severe patients (requiring oxygen or ventilation) and non hypoxemic patients. Results Seventy-two patients were included, 27 were LTR, 25 had a hematological malignancy or were hematopoietic stem cell recipients, 20 had another immunocompromised status. Twenty patients (28%) presented a hypoxemic infection, requiring hospitalization and intensive care units transfers in 50/72 (69.4%) and 9/72 (12.5%) respectively, with only one death. Hypoxemia was less pronounced in LTRs (p = 0.014). Finally, age and dyspnea remained independent factors associated with hypoxemia (p < 0.005). The most frequent radiological patterns were bronchopneumonia (34.2%) and bronchiolitis (39.5% and 64.3% in the overall population and in LTRs respectively, p = 0.045). FEV1 improved in LTRs at one month and 85% had recovered their baseline FEV1 within 6 months. Interpretations In immunocompromised adults, HMPV infections required frequent hospitalizations and ICU transfers, while mortality is low. In LTRs, bronchiolitis pattern was predominant with short and long-term favorable outcome.

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.

Background: The incidence of Enterococcus faecalis infective endocarditis is increasing over time. Data on the impact of minimum inhibitory concentration (MIC) of amoxicillin on treatment outcomes are scarce. The objective of this study was to describe the epidemiology of E. faecalis infective endocarditis and to evaluate whether the MIC of amoxicillin might influence mortality. Materials: We retrospectively included all consecutive patients diagnosed with definite E. faecalis infective endocarditis between 2013 and 2020 in 11 French hospitals. We extracted data from the local diagnosis-related group (DRG) database and matched these data with microbiologicalresults. Amoxicillin MIC was determined by Etest strip. The primary endpoints were endocarditis-related mortality and risk factors for endocarditis-related mortality including amoxicillin MIC. Results: A total of 403 patients with definite E. faecalis infective endocarditis were included. Patients were predominantly male (76.4%) with a median age of 74 years (67-82). Embolic complications occurred in 170 (42.1%) patients. Cardiac surgery was performed in 158 (61.5%) patients. The endocarditis-related mortality rate was 28.3% and the median delay between mortality and onset of hospitalization was 24 (9; 41) days. E. faecalis MIC of amoxicillin was available for 246 (61%) patients. The median MIC was 0.5 mg/L (0.4-0.7). Amoxicillin MIC was not found to be associated with in-hospital mortality. None of the variables included in the multivariate model were identified as a risk factor for mortality and there was no correlation between mortality and the duration of treatment for 4 weeks versus 6 weeks. Conclusions: Higher amoxicillin MIC was not a risk factorleading to endocarditis-related mortality in definite E. faecalis infective endocarditis. However, further studies are needed to assess the effect of amoxicillin MIC on relapse.

BACKGROUND:The duration of extensively drug-resistant bacteria (XDR) carriage depends on several factors for which the information can be difficult to recover. AIM:To determine whether past screening and clinical results of patients can predict the results of subsequent screening. METHODS:In total, 256 patients were retrospectively included from 10 healthcare centres in France from January 2014 to January 2022. We created a predictive clearance score, ranging from -5 to +7, that included the number of XDR species and the type of resistance detected in the sample, as well as the time from the last positive sample, the number of previous consecutive negative samples, and obtaining at least one negative PCR result in the collection. This score could be used for the upcoming rectal screening of a patient carrying an XDR as soon as the last screening sample was negative. FINDINGS:The negative predictive value was >99% for score ≤0. The median time to achieve XDR clearance was significantly shorter for a score of 0 (443 days (259-705)) than that based on previously published criteria. CONCLUSION:This predictive score shows high performance for the assessment of XDR clearance. Relative to previous guidelines, it could help to lift specific infection prevention and control measures earlier. Nevertheless, the decision should be made according to other factors, such as antimicrobial use and adherence to hand hygiene.

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.

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.

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.