Novel approaches to combat bacterial biofilms.

International audienceBiofilms formed by pathogenic bacteria and fungi are associated with a wide range of diseases, from device-related infections (such as catheters or prosthetic joints) to chronic infections occurring on native tissues (such as lung infections in cystic fibrosis patients). Biofilms are therefore responsible for an important medical and economic burden. Currently used antibiotics have mostly been developed to target exponentially growing microorganisms and are poorly effective against biofilms. In particular, even high concentrations of bactericidal antibiotics are inactive against a subset of persistent biofilm bacteria, which can cause infection recurrence despite prolonged treatments. While the search for a magic bullet antibiotic effective against both planktonic and biofilm bacteria is still active, alternative preventive and curative approaches are currently being developed either limiting adhesion or biofilm formation or targeting biofilm tolerance by killing persister bacteria. Most of these approaches are adjunctive using new molecules in combination with antibiotics. This review presents promising approaches or strategies that could improve our ability to prevent or eradicate bacterial biofilms in medical settings

Uropathogenic Proteus mirabilis and Klebsiella pneumoniae in companion animals : molecular epidemiology, antimicrobial resistance and zoonotic potential

Tese de Doutoramento em Ciências Veterinárias na Especialidade de ClínicaUrinary tract infections (UTI) are frequently diagnosed in companion animals and the increase in antimicrobial resistance leads to therapeutic limitations and public health concerns. The study of the geographic distribution of antimicrobial resistance in bacteria (n= 22 256) causing UTI in companion animals from 14 European countries showed that, in 2012-2013, the frequency of Escherichia coli and Proteus mirabilis antimicrobial resistance in Southern countries (Portugal, Spain, Italy, Greece) was significantly higher than in Northern countries (Denmark, Sweden). In a retrospective study conducted in Portugal (Lisbon), the antimicrobial resistance of clinical Enterobacteriaceae from companion animals with UTI increased significantly over 16 years (1999-2014; P < 0.001). Bacteria from companion animals with UTI harboured important antimicrobial resistance mechanisms and belonged to high-risk clonal lineages, namely third-generation cephalosporin (3GC)-resistant E. coli O25b:H4-B2-ST131, CC23 and ST648, methicilin-resistant Staphylococcus aureus CC5, methicilin-resistant Staphylococcus epidermidis CC5, high-level gentamicin-resistant Enterococcus faecalis CC6 and ampicillin-resistant Enterococcus faecium CC17. The blaCTX-M-15 gene was disseminated among 3GC-resistant K. pneumoniae from companion animals and humans with UTI. Most K. pneumoniae from companion animals where 3GC, multidrug-resistant (MDR) and belonged to the high-risk clonal lineage ST15. K. pneumoniae high-risk clonal lineages ST11, ST37 and ST147 were also detected in companion animals. 3GC-resistance in P. mirabilis from companion animals with UTI was associated with the presence of blaCMY-2, which increased significantly over time. A high number of PFGE clusters (43.6%, n = 17/39) included P. mirabilis strains from companion animals and humans. Gut colonisation by K. pneumoniae and P. mirabilis was detected in healthy dogs and humans; however, none of the strains was MDR. K. pneumoniae faecal strains from dogs belonged to ST17, ST188, ST252, ST281, ST423, ST1093, ST1241, ST3398 and ST3399. Remarkably, two colonised dogs were found to shared PFGE undistinguishable K. pneumoniae strains with one co-living human. P. mirabilis gut colonisation was significantly higher in dogs (P = 0.0329). One human/dog and one dog/dog pair shared PFGE undistinguishable P. mirabilis strains. The antimicrobial resistance frequencies reported in these studies support the need to implement antimicrobial stewardship programmes in veterinary medicine. The detection of MDR high-risk clonal lineages causing UTI in companion animals and the similarities detected in K. pneumoniae and P. mirabilis from companion animals and humans raises public health concerns and highlights the need for a One Health approach.RESUMO - Proteus mirabilis e Klebsiella pneumoniae uropatogénicos em animais de companhia : epidemiologia molecular, resistência aos antimicrobianos e potencial zoonótico - As infeções bacterianas do trato urinário (ITU) são frequentemente diagnosticadas em animais de companhia e no homem. O aumento da resistência e multirresistência aos antimicrobianos é um reconhecido problema na sociedade moderna que resulta na diminuição de opções terapêuticas. Com o crescente contacto entre os animais de companhia e o homem, a disseminação de bactérias resistentes a antimicrobianos criticamente importantes levanta também grandes preocupações de saúde pública. Seguindo o modelo utilizado pelo European Centre for Disease Prevention and Control (ECDC) nos relatórios de resistência aos antimicrobianos de bactérias invasivas de origem humana, o primeiro estudo apresentado nesta tese pretendeu avaliar a etiologia e a distribuição geográfica da resistência aos antimicrobianos em bactérias (n= 22 256) isoladas de animais de companhia com ITU em 14 países Europeus. Este estudo mostrou que, em 2012-2013, a frequência de resistência aos antimicrobianos em Escherichia coli e Proteus mirabilis era significativamente superior nos países estudados do Sul da Europa (Portugal, Espanha, Itália e Grécia) quando comparada com os países estudados do Norte da Europa (Dinamarca e Suécia). O mesmo aconteceu quanto a E. coli e P. mirabilis multirresistente (MDR). A elevada resistência aos antimicrobianos detetada em cães e gatos com ITU em Portugal (Lisboa) motivou a realização de um segundo estudo, retrospetivo, com o objetivo de avaliar a evolução temporal da resistência aos antimicrobianos, nesta região, ao longo de um período de 16 anos (1999-2014). Este estudo confirmou a ocorrência de um aumento significativo de resistência ao longo do tempo quanto à amoxicilina/clavulanato, cefalosporinas de terceira geração (C3G), trimetoprim/sulfametoxazol, fluoroquinolonas, gentamicina e tetraciclina (P < 0,001) em Enterobacteriaceae de animais de companhia com ITU. Adicionalmente, foi detetado um aumento significativo no isolamento de Enterobacteriaceae MDR (P < 0,0001). ...info:eu-repo/semantics/publishedVersio

Urinary tract infections in multiple sclerosis

BACKGROUND: Urinary tract infections (UTIs) are commonly reported by people with multiple sclerosis (PwMS) and significantly impact quality of life. OBJECTIVE: To provide an overview of the problem of UTIs in PwMS and offer a practical approach for the diagnosis and management. METHODS: A review of the literature through a Pubmed search up to October 2015 was performed using the following keywords: multiple sclerosis, neurogenic bladder, urinary tract infections, relapse, dipsticks, culture, recurrent and prevention. RESULTS: Noteworthy topics include the definition of a confirmed symptomatic UTI as a positive urine culture defined by >10(5) colony-forming units (CFU)/mL or >10(4) CFU/mL if a urethral catheter urine sample is taken, or any count of bacteria in a suprapubic bladder puncture specimen, both in addition to symptoms including fever, pain, changes in lower urinary tract symptoms or neurological status. Urinalysis is useful to exclude a UTI; however, on its own is insufficient to confirm a UTI, for which urine culture is required. Experts advise asymptomatic UTIs should not be treated except in the context of an acute relapse. From international guidelines, there is no validated strategy to prevent recurrent UTIs in PwMS. CONCLUSION: This review provides an overview of the diagnosis, treatment and prevention of UTIs in the setting of multiple sclerosis (MS)

Le coeur numérique personnalisé

International audienceDuring the last past years, significant progress in Medical Image Analysis, in biomathematics and biophysics have led to development of the first personalized digital cardiac models. These digital models are personalized which means they can reproduce the anatomy and physiology of specific patients. They allow the quantitative analysis of the organ function and the simulation of some therapies to evaluate their expected benefit. In this article we describe some recent research work done on these topics in our project team Asclepios at Inria, in collaboration with other Inria teams (Macs, Reo, Sisyphe) and external academic, clinical and industrial partners. If a number of challenges in mathematics and informatics still have to be solved before such personalized digital cardiac models can be used in current clinical practice, these first results announce a new generation of tools in digital medicine which can contribute more widely to a more preventive and more predictive personalized medicine.Au cours de ces dernières années, des progrès importants dans l'analyse informatique des images médicales et dans la modélisation biomathématique et biophysique ont rendu possible la construction des premiers modèles numériques et personnalisés du cœur humain. Ces modèles informatiques sont personnalisés car ils reproduisent l'anatomie et la physiologie de patients spécifiques. Ils permettent d'analyser et de quantifier le fonctionnement de l'organe et de simuler certainesthérapies pour en évaluer le bénéfice espéré. Dans cet article nous décrivons des travaux de recherche récents réalisés sur ce thème au sein de l'équipe projet Asclepios à l'Inria, en collaboration avec d'autres équipes Inria (Macs, Reo, Sisyphe) et des partenaires extérieurs académiques, cliniques et industriels. Si de grands défis en modélisation informatique et mathématique doivent encore être relevés avant une utilisation clinique courante du cœur numérique personnalisé, ces premiers résultats annoncent une nouvelle génération d'outils de médecine numérique pouvant contribuer plus largement à une médecine personnalisée plus préventive et plus prédictive

Vers un patient numérique personnalisé pour le diagnostic et la thérapie guidés par l'image [Towards a personalized digital patient for diagnosis and therapy guided by image].

National audienceRecent advances in computer science and medical imaging allow the design of new computational models of the patient which are used to assist physicians. These models, whose parameters are optimized to fit in vivo acquired images, from cells to an entire body, are designed to better quantify the observations (computer aided diagnosis), to simulate the evolution of a pathology (computer aided prognosis), to plan and simulate an intervention to optimize its effects (computer aided therapy), therefore addressing some of the major challenges of medicine of 21(st) century

Optical Flow Estimation in Ultrasound Images Using a Sparse Representation

This paper introduces a 2D optical flow estimation method for cardiac ultrasound imaging based on a sparse representation. The optical flow problem is regularized using a classical gradient-based smoothness term combined with a sparsity inducing regularization that uses a learned cardiac flow dictionary. A particular emphasis is put on the influence of the spatial and sparse regularizations on the optical flow estimation problem. A comparison with state-of-the-art methods using realistic simulations shows the competitiveness of the proposed method for cardiac motion estimation in ultrasound images

Cardiac Motion Estimation with Dictionary Learning and Robust Sparse Coding in Ultrasound Imaging

Cardiac motion estimation from ultrasound images is an ill-posed problem that needs regularization to stabilize the solution. In this work, regularization is achieved by exploiting the sparseness of cardiac motion fields when decomposed in an appropriate dictionary, as well as their smoothness through a classical total variation term. The main contribution of this work is to robustify the sparse coding step in order to handle anomalies, i.e., motion patterns that significantly deviate from the expected model. The proposed approach uses an ADMM-based optimization algorithm in order to simultaneously recover the sparse representations and the outlier components. It is evaluated using two realistic simulated datasets with available ground-truth, containing native outliers and corrupted by synthetic attenuation and clutter artefacts

Production and characterisation of yeast cell wall preparations with binding activity against Salmonella and Escherichia coli.

A rise in food safety and production standards (e.g. the ban on antibiotics) has led to a search for alternative natural products to achieve a high yielding, safe method of meat production. Mannan oligosaccharides (MOS) are one such class of product that can potentially provide this. Abundant in the cell wall of Saccharomyces cerevisiae as well as other yeast species, MOS have the capacity to inhibit type 1 fimbriae containing pathogenic bacteria from binding to host tissue and thus prevent infection. Alterations in the growing conditions of several yeast strains, including Saccharomyces, Kluyveromyces, Candida, Schizosaccharomyces, Pichia, and Rhodotorula were examined to determine if by varying simple fermentation constituents it was possible to change yeast cell wall composition and increase its MOS content. The cell wall monosaccharide content (e.g. glucose and mannose) of a number of samples was significantly altered depending on the sole carbon source in the growth medium. However, the effect of carbon source on the cell wall monosaccharide content was strain specific. A quantitative assay to assess the efficacy of MOS type products to bind bacteria in vitro was developed. Initially, agglutination of bacteria to MOS was observed on a microscope slide for a number of type 1 fimbriae containing strains of Salmonella and Escherichia coli. The method was transferred to a 96 well plate format and optimised. The binding activity assay was shown to be repeatable and reproducible for Salmonella and E. coli strains. Yeast cell wall samples generated in this study were screened using the developed assay. S. cerevisiae 695, K. lactis 752, and Schiz. pombe 70572 cell wall samples had significantly higher binding activity than the control MOS used to develop the assay. The relationship between the yeast cell wall saccharide content and binding activity varied between strains indicating that the structure and not necessarily the quantity of the saccharides were more important in binding type 1 fimbriae containing bacteria. Analysis of the N-glycan profile of the samples with high binding activity revealed the presence of both common and unique mannan oligosaccharides. These unique mannan oligosaccharides may be responsible for the increased binding activity of these samples

Mechanisms of fimbrial Assembly via non-classical Chaperone-usher pathways And receptor recognition by fimbrial adhesins

The attachment of a pathogen to target cells is a critical step in establishing an infection. Most Gram-negative pathogens display specialized adhesive pili, or fimbriae, assembled via the dedicated classical, alternative and archaic chaperone-usher (CU) pathways from protein subunits. CU pathways represent attractive inhibition targets, as the suppression of bacterial adhesion will allow the natural clearance of the pathogen without the development of antibiotic resistance. This thesis explores the mechanism and biological significance of the polyvalent attachment of fimbrial adhesins to host cell receptors and elucidates the assembly mechanism of fimbriae via the archaic CU pathway. In this study, we focused on several medically important polyadhesins: AAF/I (Escherichia coli O4H104), Myf (Yersinia enterocolitica), and Psa (Y. pestis and Y. pseudotuberculosis). We present the atomic resolution crystal structures of the fiber forming subunits of these organelles and show that they are assembled into linear homo- (Myf and Psa) or heteropolymers (AAF/I) by donor strand complementation. Each protein subunit of these three fimbriae binds to host cell receptors, thereby establishing multipoint attachment. The AggA subunits of AAF/I bind to fibronectin via a unique positively charged surface at inter-subunit interfaces. The co-crystal structures of the subunits of Myf and Psa with galactose and choline, respectively, reveal the receptor binding sites and explain differences in the tissue tropism of pathogenic species of Yersinia. The high avidity of the attachment and the ability of polyadhesins to recognize several receptors represent a significant challenge for drug development and underlines the importance of multivalent inhibitors. To elucidate the fimbriae biogenesis via the archaic CU pathway, we determined the crystal structures of the CsuC-CsuA/B chaperone-subunit preassembly complex and self-complemented CsuA/B pilin subunit from the Csu fimbriae of Acinetobacter baumannii. We show that the biogenesis of archaic systems is strikingly different from that of the classical CU pathway. The CsuC chaperone utilizes a unique subunit anchoring mechanism involving both domains of the protein. Furthermore, CsuC maintains the CsuA/B subunit in a partially disordered state, which allows for a more flexible mode of donor strand exchange. The accessible core of the chaperone-bound subunit might represent a potential inhibition target for archaic pili assembly in bacterial pathogens.Taudinaiheuttajien kiinnittyminen kohdesoluihin infektion alkaessa on kriittinen vaihe. Useimmilla gramnegatiivisilla bakteereilla on tarttumiseen erikoistuneita fimbrioita, adhesiineja, jotka muodostuvat proteiinialayksiköistä klassisen, vaihtoehtoisen ja arkaaisen kaitsija-portieeri (chaperon-usher, CU) -eritysjärjestelmän kautta. CU-järjestelmät ovat houkuttelevia inhibition kohteita, koska bakteerien kiinnittymisen ehkäisy mahdollistaa taudinaiheuttajien luonnollisen poistamisen ilman, että kehittyy antibioottiresistenssiä. Tässä väitöskirjassa käsitellään polyadhesiinien kiinnittymismekanismia kohdereseptoreihin ja arkaaisen CU-järjestelmän mukaisia fimbrioiden muodostumisperiaatteita. Tutkimuksemme kohteena olivat lääketieteellisesti tärkeät polyadhesiinit AAF/I (Escherichia coli O4H104), Myf (Yersinia enterocolitica) ja Psa (Y. pestis ja Y. pseudotuberculosis). Ratkaisimme näiden alayksiköiden kiderakenteet atomin tarkkuudella, ja osoitimme, että alayksiköt ryhmittyvät lineaarisiin homo- (Myf ja PSA) tai heteropolymeereihin (AAF/I) donorisäikeen komplementaatio -periaatteen mukaisesti. Jokainen proteiinialayksikkö pystyy kiinnittymään isäntäsolun reseptoreihin, joten polyadhesiinit varmistavat monipistekiinnityksen. AAF/I:t käyttävät AggA- alayksiköiden välillä sijaitsevia ainutlaatuisia positiivisesti varautuneita pintoja kiinnittyäkseen fibronektiiniin. Myf-fimbrioiden alayksikön kiderakenne galaktoosin ja Psa-fimbrioiden alayksikön kiderakenne koliinin kanssa paljastivat reseptorien sitoutumiskohdat ja selittivät näiden patogeenisten Yersinioiden solutropismin erot. Fimbrioiden voimakas sitoutumiskyky ja kyky tunnistaa useita reseptoreita on merkittävä haaste lääkekehitykselle, ja korostaa multivalenttisten inhibiittorien käytön tärkeyttä. Arkaaisten CU-fimbrioiden biogeneesiä valottaaksemme olemme ratkaisseet CsuC-CsuA/B-kaitsija-alayksikkö -kompleksin ja itsekomplementoidun CsuA/B-alayksikön kiderakenteet Acinetobacter baumanniin Csu-fimbrioista. Osoitimme, että arkaaisten fimbrioiden biogeneesi eroaa olennaisesti klassisesta CU-eritysjärjestelmästä sekä molekyylirakenteeltaan että toimintamekanismiltaan. CsuC-kaitsijaproteiini käyttää ainutlaatuista alayksikön ankkurointimekanismia, johon proteiinin molemmat domainit osallistuvat. Lisäksi CsuC pitää CsuA/B-alayksikön vain osittain laskostettuna, mikä saattaa mahdollistaa joustavamman donori-säikeen vaihdon. Kaitsijaan sidotun alayksikön suojaton ydin on mahdollinen inhibiitiokohde, mikä saattaa auttaa kehittämään uusia mikrobilääkkeitä, joilla pystytään estämään arkaaisten CU-fimbrioiden muodostamista.Siirretty Doriast