Compliance with antibiotic therapy guidelines in french paediatric intensive care units: a multicentre observational study.

BACKGROUND: Bacterial infections (BIs) are widespread in ICUs. The aims of this study were to assess compliance with antibiotic recommendations and factors associated with non-compliance. METHODS: We conducted an observational study in eight French Paediatric and Neonatal ICUs with an antimicrobial stewardship programme (ASP) organised once a week for the most part. All children receiving antibiotics for a suspected or proven BI were evaluated. Newborns < 72 h old, neonates < 37 weeks, age ≥ 18 years and children under surgical antimicrobial prophylaxis were excluded. RESULTS: 139 suspected (or proven) BI episodes in 134 children were prospectively included during six separate time-periods over one year. The final diagnosis was 26.6% with no BI, 40.3% presumed (i.e., not documented) BI and 35.3% documented BI. Non-compliance with antibiotic recommendations occurred in 51.1%. The main reasons for non-compliance were inappropriate choice of antimicrobials (27.3%), duration of one or more antimicrobials (26.3%) and length of antibiotic therapy (18.0%). In multivariate analyses, the main independent risk factors for non-compliance were prescribing ≥ 2 antibiotics (OR 4.06, 95%CI 1.69-9.74, p = 0.0017), duration of broad-spectrum antibiotic therapy ≥ 4 days (OR 2.59, 95%CI 1.16-5.78, p = 0.0199), neurologic compromise at ICU admission (OR 3.41, 95%CI 1.04-11.20, p = 0.0431), suspected catheter-related bacteraemia (ORs 3.70 and 5.42, 95%CIs 1.32 to 15.07, p < 0.02), a BI site classified as "other" (ORs 3.29 and 15.88, 95%CIs 1.16 to 104.76, p < 0.03), sepsis with ≥ 2 organ dysfunctions (OR 4.21, 95%CI 1.42-12.55, p = 0.0098), late-onset ventilator-associated pneumonia (OR 6.30, 95%CI 1.15-34.44, p = 0.0338) and ≥ 1 risk factor for extended-spectrum ß-lactamase-producing Enterobacteriaceae (OR 2.56, 95%CI 1.07-6.14, p = 0.0353). Main independent factors for compliance were using antibiotic therapy protocols (OR 0.42, 95%CI 0.19-0.92, p = 0.0313), respiratory failure at ICU admission (OR 0.36, 95%CI 0.14-0.90, p = 0.0281) and aspiration pneumonia (OR 0.37, 95%CI 0.14-0.99, p = 0.0486). CONCLUSIONS: Half of antibiotic prescriptions remain non-compliant with guidelines. Intensivists should reassess on a day-to-day basis the benefit of using several antimicrobials or any broad-spectrum antibiotics and stop antibiotics that are no longer indicated. Developing consensus about treating specific illnesses and using department protocols seem necessary to reduce non-compliance. A daily ASP could also improve compliance in these situations. TRIAL REGISTRATION: ClinicalTrials.gov: number NCT04642560. The date of first trial registration was 24/11/2020.

Non-uniform sampling to enhance the performance of compact NMR for characterizing new psychoactive substances.

Efficient and robust analytical methods are needed to improve the identification and subsequent regulation of new psychoactive substances (NPS). NMR spectroscopy is a unique method able to determine the structure of small molecules such as NPS even in mixtures. However, high-field NMR analysis is associated with expensive purchase and maintenance costs. For more than a decade, compact NMR spectrometers have changed this paradigm. It was recently shown that a dedicated analytical workflow combining compact NMR and databases could identify the molecular structure of NPS, in spite of the lower spectral dispersion and sensitivity of compact spectrometers. This approach relies on 1H-13C HSQC to both recognize NPS and elucidate the structure of unknown substances. Still, its performance is limited by the need to compromise between resolution and experiment time. Here, we show that this strategy can be significantly improved by implementing non-uniform sampling (NUS) to improve spectral resolution in the 13C dimension of HSQC at no cost in terms of experiment time. Gains in the range of 3 to 4 in resolution are achieved for pure NPS and for a mixture. Finally, 2D HSQC with NUS was applied to improve the identification of NPS with the assistance of databases. The resulting method appears as a useful tool for the characterization of NPS in mixtures, which is essential for forensic laboratories.

Multicenter Retrospective Study of Vascular Infections and Endocarditis Caused by Campylobacter spp., France.

The incidence of campylobacteriosis has substantially increased over the past decade, notably in France. Secondary localizations complicating invasive infections are poorly described. We aimed to describe vascular infection or endocarditis caused by Campylobacter spp. We included 57 patients from a nationwide 5-year retrospective study on Campylobacter spp. bacteremia conducted in France; 44 patients had vascular infections, 12 had endocarditis, and 1 had both conditions. Campylobacter fetus was the most frequently involved species (83%). Antibiotic treatment involved a ß-lactam monotherapy (54%) or was combined with a fluoroquinolone or an aminoglycoside (44%). The mortality rate was 25%. Relapse occurred in 8% of cases and was associated with delayed initiation of an efficient antimicrobial therapy after the first symptoms, diabetes, and coexistence of an osteoarticular location. Cardiovascular Campylobacter spp. infections are associated with a high mortality rate. Systematically searching for those localizations in cases of C. fetus bacteremia may be warranted.

Retrospective Multicentric Study on Campylobacter spp. Bacteremia in France: The Campylobacteremia Study.

BACKGROUND: Campylobacter spp. bacteremia is a severe infection. A nationwide 5-year retrospective study was conducted to characterize its clinical features and prognostic factors. METHODS: The study included patients with Campylobacter spp. bacteremia diagnosed in 37 French hospitals participating in the surveillance network of the National Reference Center for Campylobacters and Helicobacters, from 1 January 2015 to 31 December 2019. The goal was to analyze the effects of a delay of appropriate antibiotic therapy and other risk factors on 30-day mortality rates, antibiotic resistance, patient characteristics, and prognosis according to the Campylobacter species. RESULTS: Among the 592 patients, Campylobacter jejuni and Campylobacter fetus were the most commonly identified species (in 42.9% and 42.6%, respectively). The patients were elderly (median age 68 years), and most had underlying conditions, mainly immunodepression (43.4%), hematologic cancers (25.9%), solid neoplasms (23%), and diabetes (22.3%). C. jejuni and Campylobacter coli were associated with gastrointestinal signs, and C. fetus was associated with secondary localizations. Among the 80 patients (13.5%) with secondary localizations, 12 had endocarditis, 38 vascular, 24 osteoarticular, and 9 ascitic fluid infections. The 30-day mortality rate was 11.7%, and an appropriate antibiotic treatment was independently associated with 30-day survival (odds ratio, 0.47 [95% confidence interval, .24-.93]; P = .03). The median efficient therapy initiation delay was quite short (2 days [interquartile range, 0-4 days]) but it had no significant impact on the 30-day mortality rate (P = .78). CONCLUSIONS: Campylobacter spp. bacteremia mainly occurred in elderly immunocompromised individuals with variable clinical presentations according to the species involved. Appropriate antimicrobial therapy was associated with improved 30-day survival.

Deciphering the interplay between the genotoxic and probiotic activities of Escherichia coli Nissle 1917.

Although Escherichia coli Nissle 1917 (EcN) has been used therapeutically for over a century, the determinants of its probiotic properties remain elusive. EcN produces two siderophore-microcins (Mcc) responsible for an antagonistic activity against other Enterobacteriaceae. EcN also synthesizes the genotoxin colibactin encoded by the pks island. Colibactin is a virulence factor and a putative pro-carcinogenic compound. Therefore, we aimed to decouple the antagonistic activity of EcN from its genotoxic activity. We demonstrated that the pks-encoded ClbP, the peptidase that activates colibactin, is required for the antagonistic activity of EcN. The analysis of a series of ClbP mutants revealed that this activity is linked to the transmembrane helices of ClbP and not the periplasmic peptidase domain, indicating the transmembrane domain is involved in some aspect of Mcc biosynthesis or secretion. A single amino acid substitution in ClbP inactivates the genotoxic activity but maintains the antagonistic activity. In an in vivo salmonellosis model, this point mutant reduced the clinical signs and the fecal shedding of Salmonella similarly to the wild type strain, whereas the clbP deletion mutant could neither protect nor outcompete the pathogen. The ClbP-dependent antibacterial effect was also observed in vitro with other E. coli strains that carry both a truncated form of the Mcc gene cluster and the pks island. In such strains, siderophore-Mcc synthesis also required the glucosyltransferase IroB involved in salmochelin production. This interplay between colibactin, salmochelin, and siderophore-Mcc biosynthetic pathways suggests that these genomic islands were co-selected and played a role in the evolution of E. coli from phylogroup B2. This co-evolution observed in EcN illustrates the fine margin between pathogenicity and probiotic activity, and the need to address both the effectiveness and safety of probiotics. Decoupling the antagonistic from the genotoxic activity by specifically inactivating ClbP peptidase domain opens the way to the safe use of EcN.

Efficacy of teicoplanin monotherapy following initial standard therapy in Enterococcus faecalis infective endocarditis: a retrospective cohort study.

PURPOSE: Teicoplanin is often used in Enterococcus faecalis infective endocarditis as a relay in case of penicillin side effects, or in outpatients. We assessed the efficacy of teicoplanin used as continuation therapy after initial standard treatment of E. faecalis endocarditis. METHODS: All adult patients consecutively diagnosed between 1997 and 2016 for E. faecalis endocarditis were retrospectively reviewed. Patients who received standard therapy (ST) were compared to those switched to teicoplanin to complete the treatment (teicoplanin therapy, TT). RESULTS: Seventy-one patients were enrolled: 34 in the ST group and 37 in the TT group. Amoxicillin was replaced by teicoplanin after a median duration of 18 days (IQ25 - 75 12-21). Teicoplanin (5.8 ± 2.3 mg/kg) was administered for a median duration of 29 days (IQ25 - 75 25-34). Gentamicin therapy was similar. Overall duration of antimicrobial therapy was 42 days (IQ25 - 75 35-43) in the ST group, and 46 days (IQ25 - 75 43-49) in the TT group (p = 0.001). Global and endocarditis-related mortality rates were 22/34 (65%) and 13/34 (38%) in the ST group, and 14/37 (38%) and 3/37 (8%) in the TT group (p ≤ 0.05). Relapses occurred in 2/26 patients who survived the treatment phase in the ST group (8%) and in 3/37 in the TT group (8%, p = 0.68). All relapses in the TT group occurred in patients presenting prosthetic valve endocarditis. Finally, 20 patients were cured in the ST group (59%), and 33 patients in the TT group (89%, p = 0.003). CONCLUSIONS: In E. faecalis endocarditis, the switch to teicoplanin in selected patients following an initial phase of standard treatment represents an alternative, particularly for outpatient therapy. Caution should be exercised in cases of prosthetic valve endocarditis.

Escherichia coli†ClbS is a colibactin resistance protein.

The genomic pks island codes for the biosynthetic machinery that produces colibactin, a peptide-polyketide metabolite. Colibactin is a genotoxin that contributes to the virulence of extra-intestinal pathogenic Escherichia coli and promotes colorectal cancer. In this work, we examined whether the pks-encoded clbS gene of unknown function could participate in the self-protection of E. coli-producing colibactin. A clbS mutant was not impaired in the ability to inflict DNA damage in HeLa cells, but the bacteria activated the SOS response and ceased to replicate. This autotoxicity phenotype was markedly enhanced in a clbS uvrB double mutant inactivated for DNA repair by nucleotide excision but was suppressed in a clbS clbA double mutant unable to produce colibactin. In addition, ectopic expression of clbS protected infected HeLa cells from colibactin. Thus, ClbS is a resistance protein blocking the genotoxicity of colibactin both in the procaryotic and the eucaryotic cells.

Intra-nodal injection of gentamicin for the treatment of suppurated cat scratch disease's lymphadenitis.

PURPOSE: Cat scratch disease (CSD)'s lymphadenitis may have a protracted course with painful suppuration necessitating several needle aspirations or surgical drainage. The objective of this study was to evaluate the benefit of an intra-nodal injection of gentamicin add-on oral azithromycin treatment on the outcome of suppurated CSD's lymphadenitis. METHODS: We performed a retrospective monocentric study including 51 consecutive patients diagnosed between Jan 2009 and Mar 2014 with suppurated CSD who had a positive PCR for Bartonella henselae DNA in pus collected from lymph node by needle aspiration, and who were treated with azithromycin. RESULTS: Among them, 26/51 patients (51%) received oral azithromycin only, of whom 8 patients (31%) were cured and 18 patients (69%) had complications, while 25/51 patients (49%) received an intra-nodal injection of gentamicin add-on oral azithromycin, of whom 16 patients (64 %) were cured and 9 patients (36%) had complications. In univariate analysis, the combined treatment was the only variable related to cure without complications (64 versus 31%, p = 0.01), but this difference did not remain statistically significant in multivariate analysis (OR = 3.84, 95% CI: 0.95-15.56, p = 0.06). CONCLUSIONS: Intra-nodal injection of gentamicin add-on oral azithromycin treatment might improve the outcome of patients with suppurated CSD's lymphadenitis, deserving further randomized studies.

Isolation on Chocolate Agar Culture of Legionella pneumophila Isolates from Subcutaneous Abscesses in an Immunocompromised Patient.

Cutaneous infections due to Legionella species have rarely been reported (L. J. Padrnos, J. E. Blair, S. Kusne, D. J. DiCaudo, and J. R. Mikhael, Transpl Infect Dis 16:307-314, 2014; P. W. Lowry, R. J. Blankenship, W. Gridley, N. J. Troup, and L. S. Tompkins, N Engl J Med 324:109-113, 1991; M. K. Waldor, B. Wilson, and M. Swartz, Clin Infect Dis 16:51-53, 1993). Here we report the identification of Legionella pneumophila isolates, from subcutaneous abscesses in an immunocompromised patient, that grew in an unusual medium for Legionella bacteria.

Necrotizing pneumonia in children: Report of 25 cases between 2008 and 2018 at a French tertiary care center.

BACKGROUND: Necrotizing pneumonia (NP) is a serious and rare disease in children. Pediatric data on NP are limited and the impact of the 13-valent pneumococcal conjugate vaccine has been very poorly evaluated. PATIENTS AND METHODS: We conducted a retrospective study at Toulouse University Hospital between 2008 and 2018. Children who presented with thin-walled cavities in the areas of parenchymal consolidation on imaging were included in the study. RESULTS: The incidence of NP did not decrease during this period. Bacterial identification occurred in 56% of cases (14/25) and included six cases of Streptococcus pneumoniae, five of Staphylococcus aureus, two of Streptococcus pyogenes, and one of Streptococcus viridans. Streptococcus pneumoniae NP are more frequently associated with empyema/parapneumonic effusion compared to S. aureus NP (p = 0.02). Patients with S. pyogenes NP more often required volume expansion than did S. pneumoniae cases (p = 0.03). When comparing children born before and after implementation of the 13-valent pneumococcal conjugate vaccine, we identified a relative modification of the bacterial epidemiology, with an increase in the proportion of S. pyogenes NP and S. aureus NP and a decrease in the proportion of NP caused by S. pneumoniae. CONCLUSION: Future studies are needed to assess the epidemiology of NP in children. Continued surveillance of identified pneumococcal serotypes is essential to document epidemiological changes in the coming years.

Identification of clinical Streptococcus pneumoniae isolates among other alpha and nonhemolytic streptococci by use of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system.

Discrimination between Streptococcus pneumoniae and its close relatives of the viridans group is a common difficulty in matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry-based identification. In the present study, the performances of the Vitek MS MALDI-TOF mass spectrometry system were assessed using 334 pneumococci, 166 other S. mitis group streptococci, 184 non-S. mitis group streptococci, and 19 related alpha- and nonhemolytic aerobic Gram-positive catalase-negative coccal isolates. Pneumococci had been identified by means of optochin susceptibility and bile solubility or serotyping, and other isolates mainly by use of RapidID32 Strep strips. In case of discordant or low-discrimination results, genotypic methods were used. The sensitivity of the Vitek MS for the identification of S. pneumoniae was 99.1%, since only three bile-insoluble isolates were misidentified as Streptococcus mitis/Streptococcus oralis. Conversely, two optochin-resistant pneumococci were correctly identified (specificity, 100%). Three Streptococcus pseudopneumoniae isolates were also correctly identified. Among nonpneumococcal isolates, 90.8% (n = 335) were correctly identified to the species or subspecies level and 2.4% (n = 9) at the group level. For the remaining 25 isolates, the Vitek MS proposed a bacterial species included in the list of possible species suggested by genotypic methods, except for 4 isolates which were not identified due to the absence of the species in the database. According to our study, the Vitek MS displays performance similar to that of the optochin susceptibility test for routine identification of pneumococcal isolates. Moreover, the Vitek MS is efficient for the identification of other viridans group streptococci and related isolates, provided that the species are included in the database.

Non-operative treatment of acute appendicitis in children: clinical efficacy of amoxicillin-clavulanic acid in a retrospective single-centre study.

BACKGROUND: The success rate of non-operative treatment (NOT) of acute uncomplicated appendicitis (AUA) in children varies from 65% to 95%. There are no recommendations on the appropriate antibiotic therapy. OBJECTIVE: To determine the clinical efficacy of amoxicillin-clavulanic acid for NOT of AUA in children. METHODS: Design: Cross-sectional study in a single medical centre. SETTINGS: Emergency department and Paediatric Visceral Surgery department of the Children Hospital in Toulouse, France. PATIENTS: Patients 5-15 years old who were diagnosed with appendicitis, (1) With abdominal pain and a first episode of acute appendicitis, (2) With no radiological or ultrasound evidence of appendicolith, appendiceal perforation, pelvic abscess nor peritonitis, and (3) With non-septic general aspect, were included. INTERVENTIONS: NOT consisted of hospital admission. The antibiotic treatment was a combination of amoxicillin and clavulanic acid (80 mg/kg/day of amoxicillin): intravenous regimen during 48 hours followed by oral route during 7 days. MAIN OUTCOME MEASURE: Success rate of amoxicillin-clavulanic acid NOT in children with AUA at 2 years. RESULTS: The initial success rate of amoxicillin-clavulanic acid NOT in children with AUA was 100% (104/104 patients). The success rate at 2 years was 85.6% (89/104) at discharge. None of the 15 patients who underwent surgery after recurrence of appendicitis presented with peritonitis, appendiceal perforation nor pelvic abscess. CONCLUSION: Narrowed antibiotic therapy with amoxicillin and clavulanic acid seems to be an alternative to surgery in children with AUA. It is necessary to wait for the results of ongoing studies to confirm these results.

Dynamics of the digestive acquisition of bacterial carriage and integron presence by French preterm newborns according to maternal colonization: The DAIR3N multicentric study.

Objectives: The study aimed to describe the dynamics and risk factors of Gram-negative bacteria (GNB) acquisition in preterm infants. Methods: This prospective multicenter French study included mothers hospitalized for preterm delivery and their newborns, followed until hospital discharge. Maternal feces and vaginal fluids at delivery, and neonatal feces from birth to discharge were tested for cultivable GNB, potential acquired resistance, and integrons. The primary outcome was the acquisition of GNB and integrons in neonatal feces, and their dynamics, evaluated by survival analysis using the actuarial method. Risk factors were analyzed using Cox models. Results: Two hundred thirty-eight evaluable preterm dyads were included by five different centers over 16 months. GNB were isolated in 32.6% of vaginal samples, with 15.4% of strains producing extended-spectrum beta-lactamase (ESBL) or hyperproducing cephalosporinase (HCase), and in 96.2% of maternal feces, with 7.8% ESBL-GNB or HCase-GNB. Integrons were detected in 40.2% of feces and 10.6% of GNB strains. The mean (SD) length of stay of newborns was 39.5 (15.9) days; 4 died in the hospital. At least one infection episode occurred in 36.1% of newborns. The acquisition of GNB and integrons was progressive from birth to discharge. At discharge, half of newborns had ESBL-GNB or HCase-GNB, independently favored by a premature rupture of membranes (Hazard Ratio (HR), 3.41, 95% confidence interval (CI), 1.71; 6.81), and 25.6% had integrons (protective factor: multiple gestation, HR, 0.367, 95% CI, 0.195; 0.693). Conclusion: In preterm newborns, the acquisitions of GNB, including resistant ones, and integrons are progressive from birth to discharge. A premature rupture of membranes favored the colonization by ESBL-GNB or Hcase-GNB.

ClbP is a prototype of a peptidase subgroup involved in biosynthesis of nonribosomal peptides.

The pks genomic island of Escherichia coli encodes polyketide (PK) and nonribosomal peptide (NRP) synthases that allow assembly of a putative hybrid PK-NRP compound named colibactin that induces DNA double-strand breaks in eukaryotic cells. The pks-encoded machinery harbors an atypical essential protein, ClbP. ClbP crystal structure and mutagenesis experiments revealed a serine-active site and original structural features compatible with peptidase activity, which was detected by biochemical assays. Ten ClbP homologs were identified in silico in NRP genomic islands of closely and distantly related bacterial species. All tested ClbP homologs were able to complement a clbP-deficient E. coli mutant. ClbP is therefore a prototype of a new subfamily of extracytoplasmic peptidases probably involved in the maturation of NRP compounds. Such peptidases will be powerful tools for the manipulation of NRP biosynthetic pathways.

Performances of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid identification of bacteria in routine clinical microbiology.

Rapid and cost-effective matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based systems will replace conventional phenotypic methods for routine identification of bacteria. We report here the first evaluation of the new MALDI-TOF MS-based Vitek MS system in a large clinical microbiology laboratory. This system uses an original spectrum classifier algorithm and a specific database designed for the identification of clinically relevant species. We have tested 767 routine clinical isolates representative of 50 genera and 124 species. Vitek MS-based identifications were performed by means of a single deposit on a MALDI disposable target without any prior extraction step and compared with reference identifications obtained mainly with the VITEK2 phenotypic system; if the identifications were discordant, molecular techniques provided reference identifications. The Vitek MS system provided 96.2% correct identifications to the species level (86.7%), to the genus level (8.2%), or within a range of species belonging to different genera (1.3%). Conversely, 1.3% of isolates were misidentified and 2.5% were unidentified, partly because the species was not included in the database; a second deposit provided a successful identification for 0.8% of isolates unidentified with the first deposit. The Vitek MS system is a simple, convenient, and accurate method for routine bacterial identification with a single deposit, considering the high bacterial diversity studied and as evidenced by the low prevalence of species without correct identification. In addition to a second deposit in uncommon cases, expanding the spectral database is expected to further enhance performances.

Characterization of new psychoactive substances by integrating benchtop NMR to multi-technique databases.

New psychoactive substances (NPS) have become a serious threat for public health due to their ability to be sold in the street or on internet. NPS are either derived from commercial drugs which are misused (recreational rather than medical use) or whose structure is slightly modified. To regulate NPS, it is essential to accurately characterize them, either to recognize molecules that were previously identified or to quickly elucidate the structure of unknown ones. Most approaches rely on the determination of the exact mass obtained by high-resolution mass spectrometry requiring expensive equipment. This motivated us to develop a workflow in which the elucidation is assisted with databases and does not need the exact mass. This workflow combines 1D and 2D NMR measurements performed on a benchtop spectrometer with IR spectroscopy, for creating a multi-technique database to characterize pure and mixed NPS. The experimental database was created with 57 entries mostly coming from seizures, mainly cathinones, cannabinoids, amphetamines, arylcyclohexylamines, and fentanyl. A blind validation of the workflow was carried out on a set of six unknown seizures. In the first three cases, AF, AB-FUBINACA, and a mixture of 2C-I and 2C-E could be straightforwardly identified with the help of their reference spectra in the database. The two next samples were elucidated for the first time with the help of the database to reveal NEK and MPHP substances. Finally, a precise quantification of each characterized NPS was obtained in order to track NPS trafficking networks.

Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex.

Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the 'S. marcescens complex'), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila, S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum ß-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.

Cyclomodulins in urosepsis strains of Escherichia coli.

Determinants of urosepsis in Escherichia coli remain incompletely defined. Cyclomodulins (CMs) are a growing functional family of toxins that hijack the eukaryotic cell cycle. Four cyclomodulin types are actually known in E. coli: cytotoxic necrotizing factors (CNFs), cycle-inhibiting factor (Cif), cytolethal distending toxins (CDTs), and the pks-encoded toxin. In the present study, the distribution of CM-encoding genes and the functionality of these toxins were investigated in 197 E. coli strains isolated from patients with community-acquired urosepsis (n = 146) and from uninfected subjects (n = 51). This distribution was analyzed in relation to the phylogenetic background, clinical origin, and antibiotic resistance of the strains. It emerged from this study that strains harboring the pks island and the cnf1 gene (i) were strongly associated with the B2 phylogroup (P, <0.001), (ii) frequently harbored both toxin-encoded genes in phylogroup B2 (33%), and (iii) were predictive of a urosepsis origin (P, <0.001 to 0.005). However, the prevalences of the pks island among phylogroup B2 strains, in contrast to those of the cnf1 gene, were not significantly different between fecal and urosepsis groups, suggesting that the pks island is more important for the colonization process and the cnf1 gene for virulence. pks- or cnf1-harboring strains were significantly associated with susceptibility to antibiotics (amoxicillin, cotrimoxazole, and quinolones [P, <0.001 to 0.043]). Otherwise, only 6% and 1% of all strains harbored the cdtB and cif genes, respectively, with no particular distribution by phylogenetic background, antimicrobial susceptibility, or clinical origin.

Identification of a variety of Staphylococcus species by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Whole-cell fingerprinting by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) in combination with a dedicated bioinformatic software tool (MALDI Biotyper 2.0) was used to identify 152 staphylococcal strains corresponding to 22 staphylococcal species. Spectra of the 152 isolates, previously identified at the species level using a sodA gene-based oligonucleotide array, were analyzed against the main spectra of 3,030 microorganisms. A total of 151 strains out of 152 (99.3%) were correctly identified at the species level; only one strain was identified at the genus level. The MALDI-TOF MS method revealed different clonal lineages of Staphylococcus epidermidis that were of either human or environmental origin, which suggests that the MALDI-TOF MS method could be useful in the profiling of staphylococcal strains. The topology of the dendrogram generated by the MALDI Biotyper 2.0 software from the spectra of 120 Staphylococcus reference strains (representing 36 species) was in general agreement with that inferred from the 16S rRNA gene-based analysis. Our findings indicate that the MALDI-TOF MS technology, associated with a broad-spectrum reference database, is an effective tool for the swift and reliable identification of Staphylococci.

Evolution of Gut Microbiome and Metabolome in Suspected Necrotizing Enterocolitis: A Case-Control Study.

BACKGROUND: Necrotizing enterocolitis (NEC) is a devastating condition in preterm infants due to multiple factors, including gut microbiota dysbiosis. NEC development is poorly understood, due to the focus on severe NEC (NEC-2/3). METHODS: We studied the gut microbiota, microbiome and metabolome of children with suspected NEC (NEC-1). RESULTS: NEC-1 gut microbiota had a higher abundance of the Streptococcus (second 10-days of life) and Staphylococcus (third 10-days of life) species. NEC-1 children showed a microbiome evolution in the third 10-days of life being the most divergent, and were associated with a different metabolomic signature than in healthy children. The NEC-1 microbiome had increased glycosaminoglycan degradation and lysosome activity by the first 10-days of life, and was more sensitive to childbirth, low birth weight and gestational age, than healthy microbiome. NEC-1 fecal metabolome was more divergent by the second month of life. CONCLUSIONS: NEC-1 gut microbiota and microbiome modifications appear more distinguishable by the third 10-days of life, compared to healthy children. These data identify a precise window of time (i.e., the third 10-days of life) and provide microbial targets to fight/blunt NEC-1 progression.