Trends of extended-spectrum β-lactamase-producing Escherichia coli sequence type 131 and its H30 subclone in a French hospital over a 15-year period.
International audience; Sequence type 131 (ST131) is a predominant lineage among extraintestinal pathogenic Escherichia coli. It plays a major role in the worldwide dissemination of E. coli producing extended-spectrum β-lactamases (ESBLs). Here we describe the long-term epidemiology of this clonal group in a French university hospital, where the incidence of ESBL-producing E. coli has increased from 0.018 case per 1000 patient-days in the year 2000 to 0.50 case per 1000 patient-days in 2014. The first of the 141 ST131 isolates was recovered in 2006, and the ST131 clonal group accounted for 18.1% of total ESBL-producing E. coli over the whole period (2000-2014). Subclonal typing showed that …
No effect of vancomycin MIC ≥ 1.5 mg/L on treatment outcome in methicillin-susceptible Staphylococcus aureus bacteraemia
International audience; The vancomycin minimum inhibitory concentration (MIC) has been shown to affect the outcome of methicillin-susceptible Staphylococcus aureus (MSSA) bacteraemia. In this study, the outcomes of patients with MSSA bacteraemia with a vancomycin MIC ≥ 1.5 mg/L were assessed. A prospective cohort of patients with MSSA bacteraemia in two tertiary-care hospitals was collected. The vancomycin MIC was determined by Etest. Staphylococcus aureus strains were categorised as low (<1.5 mg/L) or high (≥1.5 mg/L) vancomycin MIC. First- and second-line treatments were recorded and classified as optimal, appropriate and inappropriate. The primary endpoint was 30-day mortality. A total o…
High genetic diversity among methicillin-susceptible Staphylococcus pseudintermedius in dogs in Europe.
International audience
High Prevalence of Human-Associated Escherichia coli in Wetlands Located in Eastern France
International audience; Escherichia coli that are present in the rivers are mostly brought by human and animal feces. Contamination occurs mostly through wastewater treatment plant (WWTP) outflows and field amendment with sewage sludge or manure. However, the survival of these isolates in river-associated wetlands remains unknown. Here, we assessed E. coli population structure in low-anthropized wetlands located along three floodplains to identify the major source of contamination of wetlands, whose functioning is different from the rivers. We retrieved 179 E. coli in water samples collected monthly from 19 sites located in eastern France over 1 year. Phylogroups B1 and B2 were dominant in …
Rapid antibiotic susceptibility testing on blood cultures using MALDI-TOF MS
International audience; Antibiotic resistance is a major public health problem requiring the early optimization of antibiotic prescriptions. Matrix-Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS) has been shown to accurately identify bacteria from positive blood culture. Here, we developed a rapid detection of Escherichia coli resistance to amoxicillin (AMX) and cefotaxime (CTX) from positive blood culture based on MALDI-TOF MS. Potential sparing of broad-spectrum antibiotics was also evaluated. We tested 103 E. coli-positive blood cultures. Blood cultures were subculture 1-hour in antibiotic-free rich liquid media before further incubation with and with…
Combined Bacteriophage and Antibiotic Treatment Prevents Pseudomonas aeruginosa Infection of Wild Type and cftr- Epithelial Cells
International audience; With the increase of infections due to multidrug resistant bacterial pathogens and the shortage of antimicrobial molecules with novel targets, interest in bacteriophages as a therapeutic option has regained much attraction. Before the launch of future clinical trials, in vitro studies are required to better evaluate the efficacies and potential pitfalls of such therapies. Here we studied in an ex vivo human airway epithelial cell line model the efficacy of phage and ciprofloxacin alone and in combination to treat infection by Pseudomonas aeruginosa. The Calu-3 cell line and the isogenic CFTR knock down cell line (cftr-) infected apically with P. aeruginosa strain PAO…
The rise and the fall of a Pseudomonas aeruginosa endemic lineage in a hospital
The biological features that allow a pathogen to survive in the hospital environment are mostly unknown. The extinction of bacterial epidemics in hospitals is mostly attributed to changes in medical practice, including infection control, but the role of bacterial adaptation has never been documented. We analysed a collection of Pseudomonas aeruginosa isolates belonging to the Besançon Epidemic Strain (BES), responsible for a 12year nosocomial outbreak, using a genotype-to-phenotype approach. Bayesian analysis estimated the emergence of the clone in the hospital 5 years before its opening, during the creation of its water distribution network made of copper. BES survived better than the refe…
What happens in hospitals does not stay in hospitals: antibiotic-resistant bacteria in hospital wastewater systems.
Hospitals are hotspots for antimicrobial-resistant bacteria (ARB) and play a major role in both their emergence and spread. Large numbers of these ARB will be ejected from hospitals via wastewater systems. In this review, we present quantitative and qualitative data of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, vancomycin-resistant enterococci and Pseudomonas aeruginosa in hospital wastewaters compared to community wastewaters. We also discuss the fate of these ARB in wastewater treatment plants and in the downstream environment. Published studies have shown that hospital effluents contain ARB, the burden of these bacteria being dependent on their local prevalence. The…
Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software
Next-generation sequencing (NGS) is now widely used in microbiology to explore genome evolution and the structure of pathogen outbreaks. Bioinformatics pipelines readily detect single-nucleotide polymorphisms or short indels. However, bacterial genomes also evolve through the action of small transposable elements called insertion sequences (ISs), which are difficult to detect due to their short length and multiple repetitions throughout the genome. We designed panISa software for the ab initio detection of IS insertions in the genomes of prokaryotes. PanISa has been released as open source software (GPL3) available from https://github.com/bvalot/panISa. In this study, we assessed the utilit…
mcr-1- like detection in commensal Escherichia coli and Salmonella spp. from food-producing animals at slaughter in Europe
International audience; We evaluate here the presence of the mcr-1-like and mcr-2 genes in Escherichia coli and Salmonella spp. isolated from healthy food-producing animals at slaughter between 2002 and 2014 in Europe. Isolates were retrieved from cattle, pig and chicken from 11 European countries of production. The susceptibility to colistin and antibiotics used in human medicine was determined by agar dilution. Colistin-resistant isolates were PCR-screened for mcr genes. mcr-positive isolates were typed by Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing. Among the 10,206 E. coli and 1774 Salmonella spp. isolated from cattle, pigs and chickens, 148 E. coli and 92 Sa…
Comparison of pulsed-field gel electrophoresis and whole-genome-sequencing-based typing confirms the accuracy of pulsed-field gel electrophoresis for the investigation of local Pseudomonas aeruginosa outbreaks
Summary Aim To determine whether pulsed-field gel electrophoresis (PFGE) accurately recognizes isolates belonging to clusters defined by techniques based on whole-genome sequencing (WGS) using Pseudomonas aeruginosa as a model. Methods We selected 65 isolates of ST395 P. aeruginosa isolated in seven European hospitals between 1998 and 2012. Isolates were typed by PFGE and sequenced by WGS. A core genome multi-locus sequence typing (cgMLST) analysis based on 3831 genes was performed with a homemade pipeline. Findings PFGE identified eight pulsotypes and cgMLST differentiated nine clusters and nine singletons. Five cgMLST clusters and pulsotypes (31/65 isolates) coincided perfectly. Isolates …
Pyomelanin-producingPseudomonas aeruginosaselected during chronic infections have a large chromosomal deletion which confers resistance to pyocins
When bacterial lineages make the transition from free-living to permanent association with hosts, they can undergo massive gene losses, for which the selective forces within host tissues are unknown. We identified here melanogenic clinical isolates of Pseudomonas aeruginosa with large chromosomal deletions (66 to 270 kbp) and characterized them to investigate how they were selected. When compared with their wild-type parents, melanogenic mutants (i) exhibited a lower fitness in growth conditions found in human tissues, such as hyperosmolarity and presence of aminoglycoside antibiotics, (ii) narrowed their metabolic spectrum with a growth disadvantage with particular carbon sources, includin…
Which non-carbapenem antibiotics are active against extended-spectrum β-lactamase-producing Enterobacteriaceae?
In this study, the activity of 18 non-carbapenem antibiotics was evaluated against 100 extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) and 50 ESBL-producing Klebsiella pneumoniae (ESBL-Kp) isolated from urinary tract infections and bacteraemia in 2016. Minimum inhibitory concentrations (MICs) were determined using reference methods and the susceptibility profiles were defined according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) 2017 recommendations. All of the ESBL-Ec isolates were susceptible to ceftazidime/avibactam and a great majority of them were susceptible to fosfomycin (98%), piperacillin/tazobactam (97%), amikacin (97%) and nitr…
ESBL-producing Klebsiella pneumoniae in a University hospital: Molecular features, diffusion of epidemic clones and evaluation of cross-transmission.
The worldwide spread of Klebsiella pneumoniae producing extended-spectrum β-lactamase (ESBL-Kp) is a significant threat. Specifically, various pandemic clones of ESBL-Kp are involved in hospital outbreaks and caused serious infections. In that context, we assessed the phenotypic and molecular features of a collection of ESBL-Kp isolates in a French university hospital and evaluated the occurrence of potential cross-transmissions. Over a 2-year period (2017–2018), 204 non-duplicate isolates of ESBL-Kp were isolated from clinical (n = 118, 57.8%) or screening (n = 86, 42.2%) sample cultures. These isolates were predominantly resistant to cotrimoxazole (88.8%) and ofloxacin (82.8%) but remaine…
Can MALDI-TOF Mass Spectrometry Reasonably Type Bacteria?
International audience; Bacterial typing is crucial to tackle the spread of bacterial pathogens but current methods are time-consuming and costly. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been recently integrated into the microbiology laboratory workflow for a quick and low-cost microbial species identification. Independent research groups have successfully redirected the original function of this technology from their primary purpose to discriminate subgroups within pathogen species. However, identical bacterial subgroups could be identified by unrelated peaks by independent methods, thus limiting their robustness and exportability. We…
High susceptibility of MDR and XDR Gram-negative pathogens to biphenyl-diacetylene-based difluoromethyl-allo-threonyl-hydroxamate LpxC inhibitors
International audience; Inhibitors of uridine diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC, which catalyses the first, irreversible step in lipid A biosynthesis) are a promising new class of antibiotics against Gram-negative bacteria. The objectives of the present study were to: (i) compare the antibiotic activities of three LpxC inhibitors (LPC-058, LPC-011 and LPC-087) and the reference inhibitor CHIR-090 against Gram-negative bacilli (including MDR and XDR isolates); and (ii) investigate the effect of combining these inhibitors with conventional antibiotics.MethodsMICs were determined for 369 clinical isolates (234 Enterobacteriaceae and 135 non-fermentati…
Contamination of a hospital plumbing system by persister cells of a copper-tolerant high-risk clone of Pseudomonas aeruginosa
Abstract Background Pseudomonas aeruginosa (PA) is an important opportunistic pathogen that thrives best in the distal elements of plumbing and waste-water systems. Although nosocomial outbreaks of PA have been associated with water sources, the role of the plumbing system of healthcare premises as a reservoir for this pathogen is still unclear. Materials and methods We collected water samples from 12 technical areas, distant from any medical activity, in a teaching hospital in France once a week for 11 weeks. We used a method that resuscitates persister cells because of the nutrient-poor conditions and the presence of inhibitors (e.g. chlorine and copper ions). Briefly, water was sampled i…
Genomic characterization of a local epidemic Pseudomonas aeruginosa reveals specific features of the widespread clone ST395
International audience; Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen with several clones being frequently associated with outbreaks in hospital settings. ST395 is among these so-called 'international' clones. We aimed here to define the biological features that could have helped the implantation and spread of the clone ST395 in hospital settings. The complete genome of a multidrug resistant index isolate (DHS01) of a large hospital outbreak was analysed. We identified DHS01-specific genetic elements, among which were identified those shared with a panel of six independent ST395 isolates responsible for outbreaks in other hospitals. DHS01 has the fifth largest chromosome of …
Genome analysis of enterobacteriaceae with non-wild type susceptibility to third-generation cephalosporins recovered from diseased dogs and cats in Europe
Extended-spectrum-β-lactamases (ESBL) and plasmid-mediated cephalosporinases (pAmpC)-producing Enterobacteriaceae isolates are now reported worldwide in humans, animals, and in the environment. We identified the determinants of resistance to β-lactams and associated resistance genes as well as phylogenetic diversity of 53 ESBL- or pAmpC-producing Enterobacteriaceae isolated from dogs and cats in Europe.Of a collection of 842 Enterobacteriaceae isolates that were recovered in 2013 and 2014 from 842 diseased and untreated dogs and cats, for 242 ampicillin or amoxicillin resistant isolates (MIC ≥ 16 mg/L), cefotaxime (CTX) and ceftazidime (CAZ) MICs were determined. Isolates with CTX and/or CA…
Carbapenem-Susceptible OXA-23-Producing Proteus mirabilis in the French Community
International audience; Nineteen Proteus mirabilis isolates producing the carbapenemase OXA-23 were recovered over a 2-year period in 19 French hospitalized patients, of whom 12 had community onset infections. The isolates exhibited a slightly reduced susceptibility to carbapenems. Whole-genome analysis revealed that all 19 isolates formed a cluster compared to 149 other P. mirabilis isolates. Because of its susceptibility to carbapenems, this clone may be misidentified as a penicillinase producer while it constitutes a reservoir of the OXA-23-encoding gene in the community.
ePTFE ‐based biomedical devices: An overview of surgical efficiency
International audience; Polytetrafluoroethylene (PTFE) is a ubiquitous material used for implants and medical devices in general because of its high biocompatibility and inertness: blood vessel, heart, table jawbone, nose, eyes, or abdominal wall can benefit from its properties in case of disease or injury. Its expanded version, ePTFE is an improved version of PTFE with better mechanical properties, which extends its medical applications. A material as frequently used as ePTFE with these exceptional properties deserves a review of its main uses, developments, and possibility of improvements. In this systematic review, we examined clinical trials related to ePTFE-based medical devices from t…
Enhanced emergence of antibiotic-resistant pathogenic bacteria after in vitro induction with cancer chemotherapy drugs.
International audience; BACKGROUND:Infections with antibiotic-resistant pathogens in cancer patients are a leading cause of mortality. Cancer patients are treated with compounds that can damage bacterial DNA, potentially triggering the SOS response, which in turn enhances the bacterial mutation rate. Antibiotic resistance readily occurs after mutation of bacterial core genes. Thus, we tested whether cancer chemotherapy drugs enhance the emergence of resistant mutants in commensal bacteria.METHODS:Induction of the SOS response was tested after the incubation of Escherichia coli biosensors with 39 chemotherapeutic drugs at therapeutic concentrations. The mutation frequency was assessed after …
Using GFP-Tagged Escherichia coli to Investigate the Persistence of Fecal Bacteria in Vegetated Wetlands: An Experimental Approach
The contamination of surface water by pathogenic bacteria of human origin is an important public health issue. Wetlands can be contaminated with fecal bacteria by water originating from different sources, such as wastewater treatment plants and agriculture. Escherichia coli is a commensal of the human gut flora and the major indication of fecal contamination in surface water. Little is known about the association between fecal bacteria and submerged macrophytes and how this may influence the water quality. We questioned whether macrophytes enhance or inhibit the bacterial growth in wetlands. For this purpose, we grew four different species of macrophytes (Mentha aquatica, Baldellia ranuncul…
Antimicrobial susceptibility of nine udder pathogens recovered from bovine clinical mastitis milk in Europe 2015–2016: VetPath results
International audience; VetPath is an ongoing pan-European antimicrobial susceptibility monitoring programme collecting pathogens from diseased cattle, pigs and poultry not recently treated with antibiotics. Non-duplicate isolates (n = 1244) were obtained from cows with acute clinical mastitis in eight countries during 2015-2016 for centrally antimicrobial susceptibility testing according CLSI standards. Among Escherichia coli (n = 225), resistance was high to ampicillin and tetracycline, moderate to kanamycin and low to amoxicillin/clavulanic acid and cefazolin. The MIC50/90 of danofloxacin, enrofloxacin and marbofloxacin were 0.03 and 0.06 μg/mL. For Klebsiella spp. (n = 70), similar resu…
Detection of Temporal Clusters of Healthcare-Associated Infections or Colonizations with Pseudomonas aeruginosa in Two Hospitals: Comparison of SaTScan and WHONET Software Packages.
International audience; The identification of temporal clusters of healthcare-associated colonizations or infections is a challenge in infection control. WHONET software is available to achieve these objectives using laboratory databases of hospitals but it has never been compared with SaTScan regarding its detection performance. This study provided the opportunity to evaluate the performance of WHONET software in comparison with SaTScan software as a reference to detect clusters of Pseudomonas aeruginosa. A retrospective study was conducted in two French university hospitals. Cases of P. aeruginosa colonizations or infections occurring between 1st January 2005 and 30th April 2014 in the fi…
High prevalence and moderate diversity of Pseudomonas aeruginosa in the U-bends of high-risk units in hospital
The presence of P. aeruginosa in water supply is clearly identified as a risk factor for P. aeruginosa infection in critical care units, even if routes of transmission are often unclear and remain a matter of debate. We determined here the frequency of U-bends contaminated with P. aeruginosa in high-risk units and described the population structure of this opportunistic pathogen in a non-outbreak situation. Eighty-seven U-bends from sinks of rooms in five wards were sampled 3 times and P. aeruginosa was detected in 121 of the 261 (46.4%) U-bend samples. We genotyped 123 P. aeruginosa isolates with pulsed-field gel electrophoresis and multilocus sequence typing and found 41 pulsotypes distri…
Populations of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae are different in human-polluted environment and food items: a multicentre European study
Abstract Objectives To assess the extent to which food items are a source of extended-spectrum β-lactamase (ESBL) -producing Escherichia coli (ESBL-Ec) and ESBL-producing Klebsiella pneumoniae (ESBL-Kp) for humans in five European cities. Methods We sampled 122 human polluted (hp)-environments (sewers and polluted rivers, as a proxy of human contamination) and 714 food items in Besancon (France), Geneva (Switzerland), Sevilla (Spain), Tubingen (Germany) and Utrecht (The Netherlands). A total of 254 ESBL-Ec and 39 ESBL-Kp isolates were cultured. All genomes were fully sequenced to compare their sequence types (ST) and core genomes, along with the distribution of blaESBL genes and their genet…
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data.
Abstract Motivation The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data. Results PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic spec…
Outbreak of IMI-1 Carbapenemase-producing colistin-resistant Enterobacter cloacae on the French island of Mayotte (Indian Ocean)
International audience; The spread of carbapenemase-producing Enterobacteriaceae in the Southwest Indian Ocean islands is poorly known. Here we describe an outbreak of colistin-resistant Enterobacter cloacae harbouring blaIMI-1 in the French overseas department of Mayotte. Between October 2015 and January 2017, all isolates of imipenem-non-susceptible E. cloacae at Mayotte Medical Center and University Hospital of Reunion Island were screened for carbapenemase production. Positive isolates were typed by pulsed-field gel electrophoresis and whole-genome sequencing (WGS)-based multilocus sequence typing (MLST), and all β-lactamase genes were identified by PCR and sequencing. Resistance profil…
ePTFE functionalization for medical applications
Abstract Polytetrafluoroethylene (PTFE) is a ubiquitous material used in implants and medical devices in general due to its high biocompatibility and inertness; blood vessels, heart, jawbone, nose, eyes, or abdominal wall can benefit from its properties in the case of disease or injury. Its expanded version, ePTFE, is an improved version of PTFE with better mechanical properties, which extend its medical applications. However, ePTFE implants often lack improvement in properties such as antibacterial, antistenosis, or tissue integration properties. Improvements in these properties by several strategies of functionalization for medical purposes are discussed in this review. Covalent and non-c…
The rise and the fall of a Pseudomonas aeruginosa epidemic lineage in a hospital
AbstractThe biological features that allow a pathogen to survive in the hospital environment are mostly unknown. The extinction of bacterial epidemics in hospitals is mostly attributed to changes in medical practice, including infection control, but the role of bacterial adaptation has never been documented. We analyzed a collection of Pseudomonas aeruginosa isolates belonging to the Besançon Epidemic Strain (BES), responsible for a 12-year nosocomial outbreak, using a genotype-to-phenotype approach. Bayesian analysis estimated the emergence of the clone in the hospital five years before its opening, during the creation of its water distribution network made of copper. BES survived better t…
Genotypic study of Citrobacter koseri , an emergent platelet contaminant since 2012 in France
International audience; Background: Transfusion-transmitted bacterial infection is a rare occurrence but the most feared complication in transfusion practices. Between 2012 and 2017, five cases of platelet concentrates (PCs) contaminated with the bacterial pathogen Citrobacter koseri (PC-Ck) have been reported in France, with two leading to the death of the recipients. We tested the possibilities of the emergence of a PC-specific clone of C. koseri (Ck) and of specific bacterial genes associated with PC contamination.Study design and methods: The phylogenetic network, based on a homemade Ck core genome scheme, inferred from the genomes of 20 worldwide Ck isolates unrelated to PC contaminati…