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The empirical therapy of community-acquired pneumonia (CAP) and complicated skin and soft tissue infections (cSSTIs) must be based on updated bacterial distribution and susceptibility data. A nationwide study consecutively collected 1288 isolates from CAP (n = 467) and cSSTIs (n = 821) from 18 French hospitals between 2012 and 2013. The MIC values of commonly used antimicrobial agents, including ceftaroline, were determined. Bacterial distribution featured Pneumococcus , Haemophilus influenzae , and Staphylococcus aureus for CAPs and S. aureus , β-hemolytic streptococci and Enterobacteriaceae for cSSTIs. Antimicrobial susceptibility testing indicated i) the sustained third-generation cephalosporins and levofloxacin activity against pneumococci and H. influenzae , ii) no methicillin-resistant Staphylococcus aureus emergence among respiratory pathogens, iii) the high in vitro activity of ceftaroline against staphylococci from cSSTIs (98.7% susceptibility), and iv) the worrisome decreasing fluoroquinolone and third-generation cephalosporin susceptibilities among Enterobacteriaceae. This laboratory-based survey depicts a contrasting situation and supports the scoring of patients for the resistant pathogen risk before empirical therapy. [ABSTRACT FROM AUTHOR]

Objectives: Nontuberculous mycobacteria (NTM) bone and joint infections (BJIs) are uncommon. We evaluated the characteristics of BJIs and identified differences according to immune status., Methods: We performed a multicenter retrospective study in France involving patients with documented NTM BJI over a 9-year period. We collected the clinical and microbiological characteristics, management, and clinical outcomes of the patients., Results: Overall, 95 patients were included, of whom 50.5% (48/95) were immunosuppressed. Tenosynovitis was more frequent in the immunocompetent group, and native arthritis more common in the immunosuppressed group. Mycobacerium marinum and M. abscessus complex were significantly more frequent in the immunocompetent group, and M. avium and M. xenopi were significantly more frequent in the immunosuppressed group. The combination of antibiotherapy with surgery tended to be more frequent in the immunocompetent than the immunosuppressed group (63.8% (30/47) vs 47.8% (22/46), respectively); of the latter, 45.7% (21/46) received antimicrobial therapy alone, a higher frequency than in the immunocompetent group (23.4%, 11/47). The median duration of antimicrobial treatment was similar in the two groups (11 months). Mortality was significantly higher in the immunosuppressed group., Conclusions: Although the clinical presentations and the NTM species involved in BJI differed according to immune status, most recovered completely after treatment., Competing Interests: Declarations 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 © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background: In recent years, Acinetobacter baumannii-calcoaceticus complex (ABC) infections have attracted attention, mainly because of the impact of carbapenem-resistant isolates in hospital-acquired infections. However, acute community-acquired ABC infections are not uncommon in warm and humid countries, where they are responsible for community-acquired infections with specific clinical features. To date, such infection has not been reported in France., Case Presentation: We report the case of a 55-year-old non-immunocompromised patient living in France with no known risk factors for community-acquired ABC infections who presented pneumonia with bloodstream infection due to wild-type A. pittii. The outcome was favorable after 7 days of antibiotic treatment with cefepime. We confirmed bacterial identification with whole-genome sequencing, and we examined the A. pitii core-genome phylogeny for genomic clusters., Conclusions: This situation is uncommon in Europe and occurred after a heat wave in France with temperatures above 38 °C. Herein, we discuss the possibility that this pneumonia may be emerging in the current context of global warming., (© 2024. The Author(s).)

Objectives: To describe the epidemiology of Klebsiella spp. meningitis in France with respect to clinical and bacteriological data., Methods: We performed a four-year multicenter, retrospective, observational study. The primary objective was to provide a clinical description of patients with Klebsiella spp. meningitis. Secondary objectives were to compare community-acquired meningitis and healthcare-associated meningitis and to analyze factors associated with mortality., Results: We enrolled 131 patients with Klebsiella spp. meningitis. Eighty-two (62.6%) infections were reported following neurosurgery. Twenty-eight strains (21.4%) were resistant to third-generation cephalosporins (3GC). The median [IQR] cellularity was 980/mm 3 [116-5550], the median protein level was 5.67 [1.62-9] g/L and the median CSF glucose level was 2.5 [0-3.4] mmol/L. The in-hospital mortality rate was 23.6%. Community-acquired meningitis isolates were more frequently susceptible to 3GC than isolates from healthcare-associated meningitis (89.2% versus 72%; P=0.04). Comorbidities reported for patients with community-acquired meningitis were mainly diabetes mellitus and liver cirrhosis. In multivariate analysis, focal neurological disorder at the time of diagnosis was the only factor associated with in-hospital mortality (P=0.01)., Conclusions: Purulent meningitis caused by Klebsiella spp. needs to be considered in patients with community-acquired meningitis and preexisting conditions, as well as in case of meningitis following neurosurgical procedures., (Copyright © 2021 Elsevier Masson SAS. All rights reserved.)

Introduction. Even though Corynebacterium aurimucosum has been described in 2002, this species has long been underestimated due to the unreliability of conventional identification methods and only a few cases of infections have been reported. Hypothesis/Gap Statement. Little is known about clinical significance and antimicrobial susceptibility profile of this uncommon species. Aim. To evaluate the clinical relevance of C. aurimucosum and its antimicrobial susceptibility profile. Methodology. All C. aurimucosum isolates, collected from 2010 to 2019 in 10 French university hospitals, were retrospectively included. Demographic, clinical and microbiological data were collected for all cases. Antimicrobial susceptibility testing was performed according to the 2019 EUCAST guidelines. Results. Fifty-seven clinical isolates of C. aurimucosum were collected in 57 patients (median age, 65.8 years; male/female sex ratio, 1.1), mostly from urine (28 %), blood culture (28 %) and bone/synovial fluid (19 %) samples. Of them, 14 cases of infection were confirmed, mainly bone and joint infections (50 %) followed by urinary tract infections (UTIs) (21 %), bacteremia (14 %), skin and soft-tissue infections (14 %). C. aurimucosum was recovered in pure culture in 36 % of cases (UTIs and bacteremia) while mixed cultures were observed for other infections. By testing 52 clinical isolates in vitro , this species appeared to be fully susceptible to linezolid and vancomycin while most isolates (>80 %) were susceptible to amoxicillin (MIC 90 , 2 µg ml -1 ), gentamicin, tetracycline and rifampicin. Both cefotaxime and ciprofloxacin seemed to have a limited activity (ca. 50 % of susceptible strains). The MIC distribution for ciprofloxacin showed a bimodal profile with a population of highly-resistant strains with MICs >2 µg ml -1 . Most isolates (>90 %) were categorized as resistant to penicillin G and clindamycin. Conclusion. C. aurimucosum should be considered as an actual opportunistic pathogen, and treatment with amoxicillin, vancomycin or linezolid should be preferred.

Purpose: Corynebacterium spp. (C. spp.) is commonly considered as a contaminant in respiratory specimens. No study has ever focused on its clinical relevance in the lower respiratory tract of patients admitted to the intensive care unit (ICU) and requiring mechanical ventilation. The aims were to describe the characteristics of ICU patients with a C. spp. positive deep respiratory specimen, to investigate the impact of C. spp. on the occurrence of pneumonia, and to evaluate the outcomes of these pneumonia., Methods: We retrospectively included all adult patients admitted to ICU in a 1000-bed University Hospital (2007-2017) who had a C. spp. positive lower respiratory tract specimen at a significant quantitative level. We used clinical, radiological, and microbiological criteria to classify the likelihood of such pneumonia., Results: Among the 31 patients included, acute respiratory failure and postoperative care after major surgery were the main reasons of admission. SAPS II was 47 [34-60]. C. spp. pneumonia was considered as probable, possible and unlikely in 10, 14, and 7 patients, respectively. Fifty-two and 94% of C. spp. strains were sensitive to amoxicillin, and vancomycin/linezolid, respectively. Seventeen patients had a complete course of antibiotic against C. spp. The overall ICU mortality was 58%., Conclusion: Corynebacterium spp seems to be responsible for authentic pneumonia in mechanically ventilated patients. It should be considered as clinically relevant when predominantly present in respiratory specimen from patients suspected with pneumonia in ICU, and empirically treated.

Background: Bacterial infective endocarditis (IE) is rarely suspected in patients with a low C-reactive protein (CRP) concentration., Aims: To address the incidence, characteristics and outcome of left-sided valvular IE with low CRP concentration., Methods: This was a retrospective analysis of cases of IE discharged from our institution between January 2009 and May 2017. The 10% lowest CRP concentration (<20mg/L) was used to define low CRP concentration. Right-sided cardiac device-related IE, non-bacterial IE, sequelar IE and IE previously treated by antibiotics were excluded., Results: Of the 469 patients, 13 (2.8%; median age 68 [61-76] years) had definite (n=8) or possible (n=5) left-sided valvular IE with CRP<20mg/L (median 9.3 [4.7-14.2] mg/L). The median white blood cell count was 6.3 (5.3-7.5) G/L. The main presentations were heart failure (n=7; 54%) and stroke (n=3; 23%). Transthoracic echocardiography (TTE) showed vegetations (n=5) or isolated valvular regurgitation (n=4). Overall, eight patients (62%) had severe valvular lesions on transoesophageal echocardiography (TOE), and nine patients (69%) underwent cardiac surgery. All patients survived at 1-year follow-up. Bacterial pathogens were documented in eight patients (streptococci, coagulase-negative Staphylococcus, Corynebacteriumjeikeium, HACEK group, Coxiella burnetii, Bartonella henselae) using blood cultures, serology or valve culture and/or polymerase chain reaction analysis., Conclusions: Left-sided valvular IE with limited or no biological syndrome is rare, but is often associated with severe valvular and paravalvular lesions. TOE should be performed in presence of unexplained heart failure, new valvular regurgitation or cardioembolic stroke when TTE is insufficient to rule out endocarditis, even in patients with a low CRP concentration., (Copyright © 2019. Published by Elsevier Masson SAS.)

In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collections containing commensal and bacteremia isolates. The preponderant phylogenetic group was B2 (59.6%), and the predominant sequence type complex (STc) was STc73. STc127 and STc141 were overrepresented and STc95 underrepresented in pneumonia isolates compared with bacteremia isolates. Pneumonia isolates carried higher proportions of virulence genes sfa/foc, papGIII, hlyC, cnf1, and iroN compared with bacteremia isolates. Virulence factor gene content and antimicrobial drug resistance were higher in pneumonia than in commensal isolates. Genomic and phylogenetic characteristics of E. coli pneumonia isolates from critically ill patients indicate that they belong to the extraintestinal pathogenic E. coli pathovar but have distinguishable lung-specific traits.

Our aim was to study Clostridium difficile infection (CDI) in peripartum women in France and compare them to cases published in the literature. We characterize these infections regarding clinico-biological features and specific risk factors in order to raise awareness for obstetricians and midwifes. Eight antepartum and six post-partum CDI cases were retrospectively studied in 6 French centers during the period between 2008 and 2013. In addition, 59 literature cases were reviewed. Cases were identified with CDI clinical symptoms associated to characteristic imagery or detection of C. difficile toxins. The key risk factors of CDI (antibiotherapy, hospitalization) and other risk factors (cesarean section, obstetric complications, corticotherapy, and underlying disease) were retrospectively collected. Most of the cases were exposed to at least one key risk factor of CDI: previous exposure to antibiotics and/or hospitalization. The post-partum cases often had cesarean section: 67% (4/6) in French cases and 89% (31/35) in literature cases. Metronidazole was the most used antibiotic. Relapses occurred in two French cases and in nine published cases. Two French cases and 15 literature cases were reported to have complications (pseudomembranous colitis, toxic megacolon, death…). Diverse C. difficile PCR ribotypes were involved, but the BI/NAP1/027 strain was not detected in the French case series contrary to the literature cases. The delay for diagnosis CDI could be long and peripartum CDI could be severe. In case of unexplained diarrhea in pregnant women, clinicians need to consider CDI and ask for research of C. difficile and its toxins in stool.

Purpose: Isolating colonies and obtaining accurate colony counts from bacterial cultures are critical steps for the optimal management of infected patients. The uncertainties in the colony count results from the bacterial cultures were evaluated by verifying the performance of the WASP inoculation system according to the International Organization for Standardization (ISO) 15189 standard., Methodology: We first (i) evaluated the cross-contamination and precision of the WASP instrument (Copan Diagnostics, Italy) and (ii) established enumeration reading grids for urine, swab, bronchopulmonary specimens (BPSs) and catheter tip cultures. Subsequently, 72 clinical samples were tested to compare the results of the WASP, PREVI Isola (bioMérieux, France) and manual inoculation methods., Results: The WASP method did not show cross-contamination. The coefficient of variation for the colony counts in the repeatability experiment was evaluated for 10 µl and 30 µl loop protocols and determined to be 29 and 14 %, respectively. The agreement between the automated and manual methods and between the automated methods for the colony counts was high (94.4 and 100 %, respectively). The WASP method yielded better isolation quality compared to the manual method (P=0.020) and to the PREVI Isola only when polymicrobial specimens were considered (P=0.014). For quantification evaluation, the measurement uncertainty was evaluated to 1.8×10 3  c.f.u. ml -1 for a suspension of Escherichia coli at 10 4 c.f.u. ml -1 ., Conclusion: We report the verification of the performance of the WASP instrument and describe a rapid procedure for achieving semi-quantitative cultures from BPSs and catheter tips. Quantitative interpretation of the bacterial cultures should be performed with caution.

Febrile neutropenia (FN) is the main reason for antibiotic prescription in hematology wards where, on the other hand, antibiotic stewardship (AS) is poorly explored. The objectives of the present study were to evaluate (1) the impact of an AS intervention on antibiotic consumption and (2) the applicability and acceptance rate of the intervention and its clinical impact. A persuasive AS intervention based on European Conference on Infection in Leukaemia (ECIL) guidelines for FN was implemented in a high-risk hematology ward in a tertiary referral public university hospital. This included the creation and diffusion of flow charts on de-escalation and discontinuation of antibiotics for FN, and the introduction in the team of a doctor dedicated to the implementation of flow charts and to antibiotic prescription revision. All consecutive patients receiving antibiotics during hospitalization were included. A segmented linear regression model was performed for the evaluation of antibiotic consumption, taking into account 1-year pre-intervention period and 6-month intervention period. Overall, 137 consecutive antibiotic prescriptions were re-evaluated, 100 prescriptions were for FN. A significant reduction of the level of carbapenem consumption was observed during the intervention period (level change (estimate coefficient ± standard error) = - 135.28 ± 59.49; p = 0.04). Applicability and acceptability of flow charts were high. No differences in terms of intensive care unit transfers, bacteremia incidence, and mortality were found. A persuasive AS intervention in hematology significantly reduced carbapenem consumption without affecting outcome and was well accepted. This should encourage further applications of ECIL guidelines for FN.

Objectives: The Enterobacter cloacae complex (Ecc), routinely referred to as "E. cloacae" in clinical microbiology, encompasses several species with 12 genetic clusters and one sequence crowd that can be identified based on hsp60 sequencing. Little is known about the pathogenicity and distribution of resistance to antibiotics among the Ecc., Methods and Results: In this prospective multicentre study, a total of 193 Ecc clinical isolates were collected from 10 academic hospitals distributed nationally across France and identified at the genetic cluster level on the basis of hsp60 sequencing. E. hormaechei isolates, which belong to clusters VI-VIII, were the largest group (53%), followed by cluster III that accounted for 28% of clinical isolates. All other Ecc clusters were present except cluster VII (E. hormaechei subsp. hormaechei). Cephalosporinase overproduction and ESBL were significantly more present in E. hormaechei (33% and 20%) than in other clusters (19% and 3%, respectively)., Conclusions: These results suggest that rapid identification of "E. cloacae" at the genetic cluster level could improve adequacy of empirical antibiotic treatment and reduce the unnecessary use of broad spectrum antibiotics., (Copyright © 2018 The British Infection Association. Published by Elsevier Ltd. All rights reserved.)

Background: The impact of Clostridium difficile infection (CDI) on healthcare costs is significant due to the extra costs of associated inpatient care. However, the specific contribution of recurrences has rarely been studied., Aim: The aim of this study was to estimate the hospital costs of CDI and the fraction attributable to recurrences in French acute-care hospitals., Methods: A retrospective study was performed for 2011 on a sample of 12 large acute-care hospitals. CDI costs were estimated from both hospital and public insurance perspectives. For each stay, CDI additional costs were estimated by comparison to controls without CDI extracted from the national DRG (diagnosis-related group) database and matched on DRG, age and sex. When CDI was the primary diagnosis, the full cost of stay was used., Findings: A total of 1067 bacteriological cases of CDI were identified corresponding to 979 stays involving 906 different patients. Recurrence(s) were identified in 118 (12%) of these stays with 51.7% of them having occurred within the same stay as the index episode. Their mean length of stay was 63.8 days compared to 25.1 days for stays with an index case only. The mean extra cost per stay with CDI was estimated at €9,575 (median: €7,514). The extra cost of CDI in public acute-care hospitals was extrapolated to €163.1 million at the national level, of which 12.5% was attributable to recurrences., Conclusion: The economic burden of CDI is substantial and directly impacts healthcare systems in France., (Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

Objectives: Isolation rates of unusual non-fermentative Gram-negative bacilli (i.e. other than Pseudomonas aeruginosa and Acinetobacter baumannii) are increasing but studies are limited to few observations. We aimed at determining risk factors for infection and influence of antibiotic treatment on the outcome., Methods: A six-month (December 1, 2008-May 31, 2009) prospective multicenter cohort study was conducted in nine French teaching hospitals. Characteristics of patients colonized or infected by unusual NF-GNB, adequacy of antimicrobial therapies, and outcome were analyzed., Results: Analysis of 158 patients (median age, 62.7 years) was conducted. Stenotrophomonas maltophilia was the predominant bacterial species isolated (39%) followed by Achromobacter group (15%) and non-baumannii Acinetobacter species (13%). Compared to colonized patients, infected ones were more frequently immunocompromised [relative risk (RR) = 1.63, (95% confidence interval (CI) = 1.02-2.60, P = 0.05)], hospitalized within the last three months [RR 1.67 (95% CI 1.09-2.58, P = 0.02)], admitted in an intensive care unit with central venous catheter [RR 1.74 (95% CI 1.15-2.63, P = 0.01)]. The overall hospital mortality concerned 28 patients (18%) but no association with inadequate antimicrobial treatment was found except in the group of S. maltophilia infected cases [RR 2.81 (95% CI 1.01-7.83, P = 0.02)]., Conclusion: Naturally carbapenems-resistant S. maltophilia is the main unusual NF-GNB pathogen in hospitalized patients, leading to inappropriate empirical antibiotic treatment at the time of emerging extended-spectrum β-lactamase-producing bacteria., (Copyright © 2012. Published by Elsevier Ltd.)

Nonfermenting Gram-negative bacilli (NF-GNB) are ubiquitous environmental opportunistic bacteria frequently misidentified by conventional phenotypic methods. The aim of this study was to determine the distribution of NF-GNB species by 16 S rRNA gene sequencing (used as reference method) and to compare performances of biochemical tests and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). From nine French hospitals, 188 NF-GNB isolates (except P. aeruginosa and A. baumannii) were prospectively collected from 187 clinical samples between December 2008 and May 2009. By using the genotypic approach, 173 (92%) and 188 (100%) isolates were identified to the species and genus level, respectively. They covered 35 species and 20 genera, with a predominance of Stenotrophomonas maltophilia, Achromobacter xylosoxidans, and Pseudomonas putida group bacteria. Of the 173 species-level identified strains, concordant identification to the species-level was obtained for 75.1%, 83% and 88.9% of isolates with API 20 NE strip, the VITEK-2 (ID-GN card) system and MALDI-TOF-MS, respectively. By excluding S. maltophilia isolates accurately identified by the three methods, genus-level identification was much higher for MALDI-TOF-MS (92.9%), compared with API 20 NE and VITEK-2 (76.2% and 80.8%, respectively). In conclusion, MALDI-TOF-MS represents a rapid, inexpensive, and accurate tool for routine identification of NF-GNB in human clinical samples.

The French National reference Laboratory for Human papillomavirus (HPV) performed in 2009 a national study in order to review the methods used to detect and identify HR HPV genotypes in microbiology laboratories. Results from this study show a great diversity in volumes of samples treated in laboratories. Among clinical indications, the most frequent is a result of ASC-US at a Pap smear. This indication in the only one covered by the National Public Insurance System and is mostly performed in laboratories from private sector. Other indications mainly correspond to research programs and are performed in public Hospitals. This study allowed also to review the adequacy between the liquid based cytology samples and the assays used for direct detection of HR HPV or identification of the genotypes present in the sample. The right tests were not carried in the right solution storage according to the recommendations from different HPV testing assays. National recommendations should be elaborated in order to improve the performance of the test used.

Objectives: The aac(6')-Ib gene encodes many variants of an aminoglycoside-acetyltransferase enzyme that is responsible for amikacin resistance. Recently, a new variant aac(6')-Ib-cr capable of modifying aminoglycosides and fluoroquinolones has been described. The aim of our study was to observe the appearance and the location of the aac(6')-Ib gene in extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae strains., Methods: Sixty-six and nine non-clonal ESBL-producing Enterobacteriaceae strains were isolated, respectively, for one 3-year period from 1999 to 2001 and one 2-month period in 2005 in a French Hospital (Paris, France)., Results: Among these isolates, 35 of them carried the aac(6')-Ib gene. Fourteen out of the aac(6')-Ib genes of the period 1 and two of the period 2 were genes cassette located within class 1 integrons, whereas 16 and 3, respectively, were outside integrons. One of these encoded an aminoglycoside-acetyltransferase enzyme leading to an acetyltransferase that confers resistance to all aminoglycosides. The new -cr variant of aac(6')-Ib was detected in three Escherichia coli isolates in 2005 always associated with CTX-M-15 enzyme., Conclusions: The aac(6')-Ib-cr gene, responsible for antibiotic resistance to two very different drugs, is emerging in ESBL-producing Enterobacteriaceae strains isolated in France especially in strains carrying the bla(CTx-M-15) gene.