520 results on '"Navarro, Ferran"'
Search Results
202. Escherichia coliSerotype O15:K52:H1 as a Uropathogenic Clone
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Prats, Guillem, Navarro, Ferran, Mirelis, Beatriz, Dalmau, David, Margall, Nuria, Coll, Pere, Stell, Adam, and Johnson, James R.
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ABSTRACTTo clarify the clinical and bacteriological correlates of urinary-tract infection (UTI) due to Escherichia coliO15:K52:H1, during a 1-year surveillance period we prospectively screened all 1,871 significant E. coliurine isolates at the Hospital de la Santa Creu i Sant Pau, Barcelona, Spain, for this serotype and assessed the epidemiological features of community-acquired UTI due to E. coliO15:K52:H1 versus other E. coliserotypes. We also compared the 25 O15:K52:H1 UTI isolates from the present study with 22 O15:K52:H1 isolates from other, diverse geographic locales and with 23 standard control strains (8 strains from the ECOR reference collection and 15 strains of nonpathogenic O:K:H serotypes) with respect to multiple phenotypic and genotypic traits. Although E. coliO15:K52:H1 caused only 1.4% of community-acquired E. coliUTIs during the surveillance period, these UTIs were more likely to present as pyelonephritis and to occur in younger hosts, with similar risk factors, than were UTIs due to other E. coliserotypes. Irrespective of geographic origin, E. coliO15:K52:H1 strains exhibited a comparatively restricted repertoire of distinctive virulence factor profiles (typically, they were positive forpapGallele II, papAallele F16, andaerand negative for sfa, afa,hly, and cnf1), biotypes, ribotypes, and amplotypes, consistent with a common clonal origin. In contrast, their antimicrobial resistance profiles were more extensive and more diverse than those of control strains. These findings indicate that E. coliO15:K52:H1 constitutes a broadly distributed and clinically significant uropathogenic clone with fluid antimicrobial resistance capabilities.
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- 2000
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203. Acquisition and horizontal diffusion of β-lactam resistance among clinically relevant microorganisms.
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Navarro, Ferran
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LACTAMS , *BETA lactamases , *MICROORGANISMS , *DIFFUSION , *BACTERIA , *MICROBIOLOGY , *DRUG resistance - Abstract
Discusses the acquisition and horizontal diffusion of β-lactam resistance among clinically relevant microorganisms. Background on β-lactams; Mechanisms by which bacteria may become resistant; Organisms that express low levels of an AmpC β-lactamase; Example of gene acquisition; Mechanisms by which transfer and uptake of resistance can occur; Participation of transposable elements in the diffusion of β-lactamases.
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- 2006
204. Comparing the in vitro efficacy of chlorhexidine and povidone-iodine in the prevention of post-surgical endophthalmitis.
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Batista, Celso Soares Pereira, Loscos-Giménez, Irene, Gámez, María, Altaba, Raul, de Miniac, Daniela, Martí, Neus, Bassaganyas, Francisca, Juanes, Elena, Rivera, Alba, and Navarro, Ferran
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POVIDONE-iodine , *ENDOPHTHALMITIS , *CHLORHEXIDINE , *INTRAVITREAL injections , *BACTERIAL growth - Abstract
Background: Intravitreal injections are a common ophthalmologic procedure. While infections following these injections are rare, they can lead to endophthalmitis, with potentially serious consequences. Various methods have been proposed to prevent endophthalmitis, including the use of antisepsis and antibiotics in patient preparation. Purpose: To evaluate the antiseptic efficacy of aqueous chlorhexidine (CHX) and povidone-iodine (PI) when used alone and in combination with lidocaine gel (LG) in vitro. Methods: Two independent experimental trials were conducted. The first trial determined the minimum inhibitory concentrations (MICs) and the minimum bactericidal concentrations (MBCs) of CHX and PI against six bacterial strains. The second trial evaluated the bactericidal efficacy of the antiseptic agents (CHX 0.1% and PI 5%) and their combination with LG against the same bacterial strains. Results: CHX was more effective than PI in reducing the number of colonies forming units (cfus) of the tested bacteria. The order in which the antiseptic and LG were administered affected their effectiveness, with CHX administered before LG resulting in greater reduction of bacterial growth. Conclusions: CHX 0.1% is more effective than PI 5% as an antiseptic agent. Application of CHX and PI prior to the use of lidocaine gel results in a more effective reduction of microorganisms. [ABSTRACT FROM AUTHOR]
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- 2024
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205. Comparison of Commensal and Clinical Isolates for Diversity of Plasmids in Escherichia coliand Klebsiella pneumoniae
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Rodríguez-Navarro, Judith, Miró, Elisenda, Brown-Jaque, Maryury, Hurtado, Juan Carlos, Moreno, Albert, Muniesa, Maite, González-López, Juan José, Vila, Jordi, Espinal, Paula, and Navarro, Ferran
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In this study, the plasmid content of clinical and commensal strains was analyzed and compared. The replicon profile was similar in both populations, except for L, M, A/C, and N (detected only in clinical strains) and HI1 (only in commensal strains). Although I1 and F were the most frequent replicons, only IncI1, sequence type 12 (ST12) was associated with blaCMY-2in both populations. In contrast, the widespread resistant IncF plasmids were not linked to a single epidemic plasmid.
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- 2020
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206. First Detection of a Carbapenem-Hydrolyzing Metalloenzyme in Two EnterobacteriaceaeIsolates in Spain
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Tórtola, M. Teresa, Lavilla, Susana, Miró, Elisenda, González, Juan José, Larrosa, Nieves, Sabaté, Montserrat, Navarro, Ferran, and Prats, Guillermo
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ABSTRACTTwo strains of Enterobacteriaceae, Escherichia coliand Klebsiella pneumoniae, producing VIM-1 were isolated for the first time in Spain. In both strains, blaVIM-1was found to be carried on a gene cassette inserted into a class 1 integron. The blaVIM-1-containing integron was located on a transferable plasmid.
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- 2005
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207. Impacte de l'energia nuclear en l'entorn
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Battestini, R., Aragón, Lina Marcela, Armengol, J., Biete Solà, Albert, Broggi, Moisès, 1908-2012, García, C., Moreno, F. X., Navarro, Ferran, and Universitat de Barcelona
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Contaminació radioactiva ,Avaluació d'impacte ambiental ,Environmental impact analysis ,Energia nuclear ,Nuclear energy ,Radioactive pollution - Abstract
El progrés científic segueix sovint uns camins que no estan exempts de risc i veiem com moltes novetats tecnològiques, inicialment acollides amb entusiasme, es converteixen en armes de dos talls, representant alhora un benefici i un risc: aquest és el cas de l'energia nuclear.
208. Identification of chromosomal rearrangements in colorectal cancer
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Moratalla Navarro, Ferran, Universitat de Vic - Universitat Central de Catalunya. Facultat de Ciències i Tecnologia, and Universitat de Vic - Universitat Central de Catalunya. Màster Universitari en Anàlisi de Dades Òmiques
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Gens del càncer ,Còlon -- Càncer - Abstract
Curs 2014-2015, Cancer research is continuously shedding light into these worldwide leading diseases. It is mandatory to have higher knowledge in cancer biology to consequently find out new candidate biomarkers and therapeutics. Among all of them, Colorectal cancer is the most commonly seen of human malignant cancers and has the third highest mortality rate[1]. Since the release of the first human genome sequence in 2004, new techniques have revolutionised the study of genetics and its possible applications. A broad type of studies has been carried out; being Single Nucleotide Polymorphisms and Copy Number Variants the most intensively studied analysis. However, other kinds of mutations involving larger parts of the genome, the so-called structural variants, have been substantially less analyzed due to technical limitations. High-throughput sequencing methods seem to have lowered these restrictions. In this study, gene fusions have been searched in whole exome sequencing samples taking 42 paired normal and cancer tissues. Beginning with short-read files obtained with the mentioned method, they have been aligned against a reference genome to later be analyzed with Breakdancer, a structural variant calling algorithm. After some filtering criteria performed in order to remove a high proportion of false positives, a highly probable list of 22 balanced structural variants (translocations and/or inversions) has been manually studied to get a final result of 20 chromosomal rearrangements, 8 of which are considered gene fusions. In addition, it has been found that one recurrent translocation seen in recent studies is indeed a false positive. Further studies taking into account these results may contribute to the findings of new biomarkers for certain subtypes of colorectal cancer., Director/a: Victor Moreno, co-director: Mireia Olivella
209. Novel insights into genetic susceptibility for colorectal cancer from transcriptome-wide association and functional investigation.
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Chen, Zhishan, Song, Wenqiang, Shu, Xiao-Ou, Wen, Wanqing, Devall, Matthew, Dampier, Christopher, Moratalla-Navarro, Ferran, Cai, Qiuyin, Long, Jirong, Kaer, Luc Van, Wu, Lan, Huyghe, Jeroen R, Thomas, Minta, Hsu, Li, Woods, Michael O, Albanes, Demetrius, Buchanan, Daniel D, Gsur, Andrea, Hoffmeister, Michael, and Vodicka, Pavel
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ALTERNATIVE RNA splicing , *COLORECTAL cancer , *GENE expression , *GENETIC engineering ,CANCER susceptibility - Abstract
Background Transcriptome-wide association studies have been successful in identifying candidate susceptibility genes for colorectal cancer (CRC). To strengthen susceptibility gene discovery, we conducted a large transcriptome-wide association study and an alternative splicing transcriptome-wide association study in CRC using improved genetic prediction models and performed in-depth functional investigations. Methods We analyzed RNA-sequencing data from normal colon tissues and genotype data from 423 European descendants to build genetic prediction models of gene expression and alternative splicing and evaluated model performance using independent RNA-sequencing data from normal colon tissues of the Genotype-Tissue Expression Project. We applied the verified models to genome-wide association studies (GWAS) summary statistics among 58 131 CRC cases and 67 347 controls of European ancestry to evaluate associations of genetically predicted gene expression and alternative splicing with CRC risk. We performed in vitro functional assays for 3 selected genes in multiple CRC cell lines. Results We identified 57 putative CRC susceptibility genes, which included the 48 genes from transcriptome-wide association studies and 15 genes from splicing transcriptome-wide association studies, at a Bonferroni-corrected P value less than .05. Of these, 16 genes were not previously implicated in CRC susceptibility, including a gene PDE7B (6q23.3) at locus previously not reported by CRC GWAS. Gene knockdown experiments confirmed the oncogenic roles for 2 unreported genes, TRPS1 and METRNL , and a recently reported gene, C14orf166. Conclusion This study discovered new putative susceptibility genes of CRC and provided novel insights into the biological mechanisms underlying CRC development. [ABSTRACT FROM AUTHOR]
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- 2024
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210. The Carbapenemase-Producing Klebsiella pneumoniaePopulation Is Distinct and More Clonal than the Carbapenem-Susceptible Population
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Esteban-Cantos, Andrés, Aracil, Belén, Bautista, Verónica, Ortega, Adriana, Lara, Noelia, Saez, David, Fernández-Romero, Sara, Pérez-Vázquez, María, Navarro, Ferran, Grundmann, Hajo, Campos, José, and Oteo, Jesús
- Abstract
ABSTRACTWe studied in parallel the population structure of 90 carbapenemase-producing and 88 carbapenemase-susceptible Klebsiella pneumoniaeisolates collected in 20 Spanish hospitals, in the context of the EuSCAPE project. Fourteen and 50 multilocus sequence types (MLSTs) were detected among the carbapenemase-producing and carbapenem-susceptible isolates, respectively. ST11 and ST15 clones were more frequent in the carbapenemase-producing group than in the carbapenemase-susceptible group (P< 0.0001). Among the members of the carbapenem-suceptible group, the cefotaxime-resistant population showed population parameters that differed between the populations of the wild-type strains and the carbapenemase producers.
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- 2017
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211. Escherichia coli Producing an ACC-1 Class C {szligbeta}-Lactamase Isolated in Barcelona, Spain
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Miró, Elisenda, Mirelis, Beatriz, Navarro, Ferran, Matas, Lurdes, Giménez, Montserrat, and Rabaza, Cinta
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- 2005
212. Escherichia coliProducing an ACC-1 Class C β-Lactamase Isolated in Barcelona, Spain
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Miró, Elisenda, Mirelis, Beatriz, Navarro, Ferran, Matas, Lurdes, Giménez, Montserrat, and Rabaza, Cinta
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- 2005
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213. Quinolone Resistance-Determining Regions of gyrAandparCin Pasteurella multocidaStrains with Different Levels of Nalidixic Acid Resistance
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Cárdenas, Maribel, Barbé, Jordi, Llagostera, Montserrat, Miró, Elisenda, Navarro, Ferran, Mirelis, Beatriz, Prats, Guillem, and Badiola, Ignasi
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- 2001
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214. Detection of three stable genetic clones of CTX-M-15-producing Klebsiella pneumoniae in the Barcelona metropolitan area, Spain.
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Coelho, Alicia, Mirelis, Beatriz, Alonso-Tarrés, Carles, Larrosa, María Nieves, Miró, Elisenda, Clivillé Abad, Raquel, Bartolomé, Rosa María, Castañer, Mireia, Prats, Guillem, Johnson, James R., Navarro, Ferran, and González-López, Juan José
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KLEBSIELLA pneumoniae ,CLONING - Abstract
A correction to the article "Detection of Three Stable Genetic Clones of CTX-M-15-Producing Klebsiella pneumoniae in the Barcelona Metropolitan Area, Spain" that was published in a 2009 issue of the journal is presented.
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- 2010
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215. Increase in Quinolone Resistance in aHaemophilus influenzaeStrain Isolated from a Patient with Recurrent Respiratory Infections Treated with Ofloxacin
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Vila, Jordi, Ruiz, Joaquim, Sanchez, Ferran, Navarro, Ferran, Mirelis, Beatriz, de Anta, M. Teresa Jimenez, and Prats, Guillem
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ABSTRACTThe increase in the level of quinolone resistance ofHaemophilus influenzaeclinical isolates during ofloxacin therapy of a patient with recurrent respiratory infections was investigated. The first isolate (MIC of ciprofloxacin of 2 μg/ml) and the second isolate (MIC of 32 μg/ml) belonged to the same clone, as shown by pulsed-field gel electrophoresis, and the increase in the resistance level was associated with a substitution in Ser-84 to Arg in the ParC protein. These results emphasize the potential risk of development of quinolone-resistant H. influenzaeduring fluoroquinolone therapy in patients with recurrent respiratory infection.
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- 1999
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216. Host‐associated variability of the cdtABC operon, coding for the cytolethal distending toxin, in Campylobacter jejuni.
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Guirado, Pedro, Iglesias‐Torrens, Yaidelis, Miró, Elisenda, Navarro, Ferran, Attolini, Camile Stephan‐Otto, Balsalobre, Carlos, and Madrid, Cristina
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CAMPYLOBACTER jejuni , *OPERONS , *TOXINS , *BROILER chickens , *CAMPYLOBACTER , *DNA primers , *GASTROINTESTINAL system - Abstract
Campylobacter, a major cause of food‐borne gastroenteritis worldwide, colonize the gastrointestinal tract of a wide range of animals, being birds the main reservoir. The mechanisms involved in the interaction of Campylobacter with the different hosts are poorly understood. The cytolethal distending toxin, encoded in the cdtABC operon, is considered a pivotal virulence factor during human infection. Differences in the prevalence of cdtABC genes in Campylobacter isolates from three distinct origins (wild birds, broiler chickens and humans) prompted us to further characterize their allelic variability. The sequence of cdtABC is highly conserved among broiler and human isolates. A high diversity of cdtABC alleles was found among wild bird isolates, including several alleles that do not produce any functional CDT. These results suggest that specific variants of the cdtABC operon might define the host range of specific Campylobacter jejuni isolates. Moreover, our data indicate that PCR methodology is inaccurate to characterize the prevalence of the cdt genes, since negative PCR detection can be the result of divergences in the sequence used for primer design rather than indicating the absence of a specific gene. [ABSTRACT FROM AUTHOR]
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- 2022
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217. Surveillance of extended-spectrum {beta}-lactamases from clinical samples and faecal carriers in Barcelona, Spain
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Miró, Elisenda, Mirelis, Beatriz, Navarro, Ferran, Rivera, Alba, Mesa, Raúl Jesús, Roig, M<SUP>a</SUP> Carme, Gómez, Laura, and Coll, Pere
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<it>Objectives</it>: The aim of the present study was to characterize and compare the extended-spectrum β-lactamase (ESBL)-producing organisms isolated from clinical samples and faecal carriers in 2001 and 2002. <it>Methods</it>: A total of 5251 Enterobacteriaceae isolated from clinical samples and 1321 stool samples were evaluated for the presence of ESBLs. The stool samples were spread onto plates of MacConkey agar containing 2 mg/L cefotaxime for selection of ESBL-producing strains. These strains were defined as those showing synergism between amoxicillin/clavulanic acid and third-generation cephalosporins. The β-lactamases involved were characterized by isoelectric focusing, PCR assays and DNA sequencing. <it>Results</it>: The prevalence of ESBL-producing strains among clinical Enterobacteriaceae was 1.7%. Of these, 87.6% produced CTX-M, 25.8% produced SHV and 2.2% were TEM-type-producing strains. All clinical ESBL-producing strains were <it>Escherichia coli</it>, with the exception of four <it>Klebsiella pneumoniae</it> and one <it>Citrobacter freundii</it>. The prevalence of faecal carriage of ESBL-producing organisms was 3.3%. Of these, 75% produced CTX-M-type enzymes followed by 22.7% SHV-producing strains. All faecal ESBL-producing strains were <it>E. coli</it> except for one <it>Enterobacter cloacae</it> and one <it>Proteus mirabilis</it>. This latter strain produced the PER-1 enzyme reported for the first time in Spain. <it>Conclusions</it>: The prevalence of ESBL-producing strains in stool samples was higher than that observed in clinical samples from the same period. The different types of ESBLs found were similar in both contexts. The most prevalent ESBLs were the CTX-M-related enzymes, with nine different types, followed by SHV-12.
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- 2005
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218. Characterization of the highly variable region surrounding the blaCTX-M-9 gene in non-related Escherichia coli from Barcelona
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García, Aurora, Navarro, Ferran, Miró, Elisenda, Mirelis, Beatriz, Campoy, Susana, and Coll, Pere
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<it>Objectives</it>: The dispersion of a clone, a plasmid or a mobile element carrying the <it>bla</it><inf>CTX-M-9</inf> gene was evaluated in 30 <it>Escherichia coli</it> strains isolated in Barcelona between 1996 and 1999. The presence of the previously described <it>orf513</it>-bearing class 1 integron, In60, carrying the <it>bla</it><inf>CTX-M-9</inf> gene, was also studied. <it>Methods</it>: The clonality was analysed by pulsed-field gel electrophoresis. Plasmid analysis was performed by S1 digestion and hybridization with the CTX-M-9 probe. PCR mapping using specific designed primers was used to study the presence of In60 and In60-like structures. <it>Results</it>: The clonality between the 30 strains was minor. The size of <it>bla</it><inf>CTX-M-9</inf> carrying plasmids ranged between ∼80 and 430 kb. One strain produced only a chromosome-encoded CTX-M-9 β-lactamase. Thirty-six per cent of the strains showed differences with respect to the In60 structure due to an insertion or deletion events. <it>Conclusions</it>: These findings suggest that the <it>bla</it> <inf>CTX-M-9</inf> gene may be carried by a mobile element that disperses it between plasmids. The fast dispersion of the CTX-M-9 enzyme could therefore be due to both diffusion of plasmids and mobile elements.
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- 2005
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219. Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes.
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Obón-Santacana, Mireia, Mas-Lloret, Joan, Bars-Cortina, David, Criado-Mesas, Lourdes, Carreras-Torres, Robert, Díez-Villanueva, Anna, Moratalla-Navarro, Ferran, Guinó, Elisabet, Ibáñez-Sanz, Gemma, Rodríguez-Alonso, Lorena, Mulet-Margalef, Núria, Mata, Alfredo, García-Rodríguez, Ana, Duell, Eric J., Pimenoff, Ville Nikolai, and Moreno, Victor
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STATISTICAL significance , *META-analysis , *CONFIDENCE intervals , *EARLY detection of cancer , *COLORECTAL cancer , *RISK assessment , *FECES , *GENOMES , *HUMAN microbiota , *DESCRIPTIVE statistics , *PREDICTION models , *RECEIVER operating characteristic curves , *PRECANCEROUS conditions , *DISEASE risk factors - Abstract
Simple Summary: Colorectal cancer (CRC) is the third most common cancer in the world. The gut microbiome, which includes a collection of microbes, is a potential modifiable risk factor. The study of the microbiome is complex and many issues remain unsolved despite the scientific efforts that have been recently made. The present study aimed to build a CRC predictive model performing a meta-analyses of previously published shotgun metagenomics data, and to validate it in a new study. For that purpose, 156 participants of a CRC screening program were recruited, with an even distribution of CRCs, high-risk colonic precancerous lesions, and a control group with normal colonic mucosa. We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions. This suggests that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. The gut microbiome is a potential modifiable risk factor for colorectal cancer (CRC). We re-analyzed all eight previously published stool sequencing data and conducted an MWAS meta-analysis. We used cross-validated LASSO predictive models to identify a microbiome signature for predicting the risk of CRC and precancerous lesions. These models were validated in a new study, Colorectal Cancer Screening (COLSCREEN), including 156 participants that were recruited in a CRC screening context. The MWAS meta-analysis identified 95 bacterial species that were statistically significantly associated with CRC (FDR < 0.05). The LASSO CRC predictive model obtained an area under the receiver operating characteristic curve (aROC) of 0.81 (95%CI: 0.78–0.83) and the validation in the COLSCREEN dataset was 0.75 (95%CI: 0.66–0.84). This model selected a total of 32 species. The aROC of this CRC-trained model to predict precancerous lesions was 0.52 (95%CI: 0.41–0.63). We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions, suggesting that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. Further studies should focus on CRC as well as precancerous lesions with the intent to implement a microbiome signature in CRC screening programs. [ABSTRACT FROM AUTHOR]
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- 2022
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220. Prevalence and seasonality of viral respiratory infections in a temperate climate region: A 24‐year study (1997–2020).
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García‐Arroyo, Laura, Prim, Núria, Del Cuerpo, Marga, Marín, Pilar, Roig, Maria Carme, Esteban, Mnontserrat, Labeaga, Rosa, Martí, Neus, Berengua, Carla, Gich, Ignasi, Navarro, Ferran, and Rabella, Núria
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TEMPERATE climate , *VIRUS diseases , *RESPIRATORY syncytial virus , *PANDEMICS , *RESPIRATORY infections , *COVID-19 pandemic , *H1N1 influenza - Abstract
Background: Few long‐term reports have been published on the epidemiology of respiratory viruses despite their frequent involvement in extremely common infections. The aim here was to determine the frequency and distribution of respiratory viruses in a temperate climate area (Barcelona, Spain) throughout a 24‐year period. Methods: We collected data on all respiratory viruses detected from 1997 to 2020 in our institution. Clinical specimens were analyzed mainly by conventional techniques, and molecular techniques were also used. Results: Of the 59,579 specimens analyzed, 21,382 (35.9%) were positive for at least one virus. The number of positive samples during cold months was significantly higher than in warm months. Respiratory virus infections were detected in patients of all ages, above all in children under 3 years of age, who were most frequently infected with the respiratory syncytial virus, whereas Influenza A virus predominated in the other groups, especially in adults. A clear demographic and seasonal pattern was established for some viruses. Circulation of other respiratory viruses during the FLUAV H1N1pdm09 and SARS‐CoV‐2 pandemics was observed. Conclusions: This long‐term study provides new knowledge about the prevalence of respiratory viruses in a Mediterranean region. Throughout the study period, the frequency of some viruses remained constant, whereas others varied with the year. A clear demographic and seasonal pattern was established for some viruses. Patients suffering from severe respiratory infections should be examined for a range of respiratory viruses regardless of gender, age, or season. [ABSTRACT FROM AUTHOR]
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- 2022
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221. Spread of plasmids containing the blaVIM-1 and blaCTX-M genes and the qnr determinant in Enterobacter cloacae, Klebsiella pneumoniae and Klebsiella oxytoca isolates.
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Miró, Elisenda, Segura, Concha, Navarro, Ferran, Sorlí, Lluisa, Coll, Pere, Horcajada, Juan P., Álvarez-Lerma, Francisco, and Salvadó, Margarita
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ENTEROBACTER cloacae , *KLEBSIELLA pneumoniae , *PLASMIDS , *NUCLEOTIDE sequence , *GENOMES , *CARBAPENEMS - Abstract
Objectives: We describe 12 VIM-1-producing strains (7 Enterobacter cloacae, 2 Klebsiella pneumoniae and 3 clonal Klebsiella oxytoca strains) detected among clinically relevant Enterobacteriaceae isolates from routine cultures at the Hospital del Mar (Barcelona, Spain) from December 2006 to May 2007. Methods: Susceptibility to carbapenems was evaluated with the MicroScan system. b-Lactamases were identified by PCR and sequencing. Clonal relationships between the isolates were analysed by PFGE. Transferability of the enzymes was tested by conjugation. Plasmid characterization was performed by PCR-based replicon typing and PFGE with S1 nuclease digestion of whole genomic DNA. The PFGE gels were then transferred and hybridized. Results: The disc diffusion method correctly identified five of the seven E. cloacae isolates as intermediate or resistant strains. All isolates produced the VIM-1 enzyme. Three E. cloacae and three K. oxytoca strains were also CTX-M-9-producing strains, and one E. cloacae was also a CTX-M-3-producing strain. The plasmids carrying the blaVIM gene, of unknown incompatibility group, had a size of ∼75 kb (eight strains) or 40 kb (three strains) and also contained the qnrS and the aac(6′)-Ib-cr genes. In the remaining strain the blaVIM-1 gene was found in an HI2 plasmid of 290 kb together with blaCTX-M-9, qnrA, qnrS and the aac(6′)-Ib-cr genes. Conclusions: The results showed a linkage between the blaVIM-1 and the qnrS and the aac(6′)-Ib-cr genes, and between the blaCTX-M-9 and the qnrA genes. [ABSTRACT FROM AUTHOR]
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- 2010
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222. In vitro and in vivo efficacy of combinations of colistin and different endolysins against clinical strains of multi-drug resistant pathogens.
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Blasco, Lucia, Ambroa, Anton, Trastoy, Rocio, Bleriot, Ines, Moscoso, Miriam, Fernández-Garcia, Laura, Perez-Nadales, Elena, Fernández-Cuenca, Felipe, Torre-Cisneros, Julian, Oteo-Iglesias, Jesus, Oliver, Antonio, Canton, Rafael, Kidd, Tim, Navarro, Ferran, Miró, Elisenda, Pascual, Alvaro, Bou, German, Martínez-Martínez, Luis, and Tomas, Maria
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MULTIDRUG resistance in bacteria , *ANTI-infective agents , *MEDICAL sciences , *BACTERIOPHAGES , *GENOMES - Abstract
The emergence of multidrug resistant (MDR) pathogenic bacteria is jeopardizing the value of antimicrobials, which had previously changed the course of medical science. In this study, we identified endolysins ElyA1 and ElyA2 (GH108-PG3 family), present in the genome of bacteriophages Ab1051Φ and Ab1052Φ, respectively. The muralytic activity of these endolysins against MDR clinical isolates (Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae) was tested using the turbidity reduction assay. Minimal inhibitory concentrations (MICs) of endolysin, colistin and a combination of endolysin and colistin were determined, and the antimicrobial activity of each treatment was confirmed by time kill curves. Endolysin ElyA1 displayed activity against all 25 strains of A. baumannii and P. aeruginosa tested and against 13 out of 17 strains of K. pneumoniae. Endolysin ElyA2 did not display any such activity. The combined antimicrobial activity of colistin and ElyA1 yielded a reduction in the colistin MIC for all strains studied, except K. pneumoniae. These results were confirmed in vivo in G. mellonella survival assays and in murine skin and lung infection models. In conclusion, combining colistin (1/4 MIC) with the new endolysin ElyA1 (350 µg) enhanced the bactericidal activity of colistin in both in vitro and in vivo studies. This will potentially enable reduction of the dose of colistin used in clinical practice. [ABSTRACT FROM AUTHOR]
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- 2020
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223. Unravelling the consequences of the bacteriophages in human samples.
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Blanco-Picazo, Pedro, Fernández-Orth, Dietmar, Brown-Jaque, Maryury, Miró, Elisenda, Espinal, Paula, Rodríguez-Rubio, Lorena, Muniesa, Maite, and Navarro, Ferran
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BACTERIOPHAGES , *HUMAN microbiota , *PATHOGENIC microorganisms , *BACTERIAL genes , *RIBOSOMAL RNA - Abstract
Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. To unravel these interferences, human samples (n = 271) were analyzed and infectious phages were observed in 11% of blood culture, 28% of serum, 45% of ascitic fluid, 14% of cerebrospinal fluid and 23% of urine samples. The genetic content of phage particles from a pool of urine and ascitic fluid samples corresponded to bacteriophages infecting different bacterial genera. In addition, many bacterial genes packaged in the phage capsids, including antibiotic resistance genes and 16S rRNA genes, were detected in the viromes. Phage interference can be minimized applying a simple procedure that reduced the content of phages up to 3 logs while maintaining the bacterial load. This method reduced the detection of phage genes avoiding the interference with molecular detection of bacteria and reduced the phage propagation in the cultures, enhancing the recovery of bacteria up to 6 logs. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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224. Faecal phageome of healthy individuals: presence of antibiotic resistance genes and variations caused by ciprofloxacin treatment.
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Fernández-Orth, Dietmar, Miró, Elisenda, Brown-Jaque, Maryury, Rodríguez-Rubio, Lorena, Espinal, Paula, Rodriguez-Navarro, Judith, González-López, Juan José, Muniesa, Maite, and Navarro, Ferran
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CIPROFLOXACIN , *ANTIBIOTICS , *NUCLEOTIDE sequencing , *DRUG resistance in bacteria , *ESCHERICHIA coli - Abstract
Objectives: Antimicrobial resistance genes (ARGs) can be transferred by means of mobile genetic elements, which play a critical role in the dissemination of resistance in the bacterial community. ARG transmission within mobile genetic elements has been reported in plasmids and transposons but less frequently in bacteriophages. Here, the bacteriophage fraction of seven human faecal samples was purified and deep-sequenced to detect the presence of ARGs in the phage particles.Methods: Seven faecal samples (five from healthy individuals and two from a patient before and after receiving ciprofloxacin treatment) were used to extract phage DNA, which was purified and then sequenced in a MiSeq (Illumina). Generated reads were checked for quality and assembled, and then the generated contigs analysed with Kraken, PHASTER, VirSorter and Prokka. Some genes were also validated by quantitative PCR.Results: Analysis of the purified phage DNA by Kraken identified from 4 to 266 viruses in the samples. The viral fraction corresponded mainly to the order Caudovirales, including phages from the Siphoviridae and Myoviridae families. Bacterial genes associated with antimicrobial resistance were detected in the viral DNA, as confirmed by quantitative PCR. Higher densities of ARG-carrying phage particles were observed in the post- versus pre-ciprofloxacin treatment sample.Conclusions: The finding of ARGs in phage particles supports the description of phages as mobile elements contributing to the dissemination of bacterial antibiotic resistance and suggests ciprofloxacin treatment may play a role in the release of ARG-carrying particles, thereby increasing resistance. [ABSTRACT FROM AUTHOR]- Published
- 2019
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225. First Description of blaNDM-7 Carried on an IncX4 Plasmid in Escherichia coli ST679 Isolated in Spain.
- Author
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Espinal, Paula, Miró, Elisenda, Segura, Concepción, Gómez, Laura, Plasencia, Virginia, Coll, Pere, and Navarro, Ferran
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ESCHERICHIA coli , *PLASMIDS , *CYTOPLASMIC inheritance , *GENETIC vectors , *PLASMID incompatibility - Abstract
This study describes the molecular characterization of an NDM-7 carbapenemase-producing Escherichia coli strain Ec188, recovered from a rectal swab of a male patient who had travelled to Pakistan before his hospitalization at the Hospital del Mar in Barcelona, Spain. The Ec188 isolate, assigned to a new multilocus sequence type ST679, was resistant to all beta-lactams, aminoglycosides (gentamicin, tobramycin, and with reduced susceptibility to amikacin), and ciprofloxacin. The blaNDM-7 gene was located on a 50 kb IncX4 plasmid (pEc188-NDM7), both in the original and transconjugant strains. In addition, blaCTX-M-15 was located on a 150 kb IncFIA plasmid and blaCMY-2 on a 95 kb undetermined plasmid type, only in the wild-type strain. The immediate genetic surroundings of blaNDM-7 included the bleo, trpf, and dsbC genes, and it was flanked by the insertion sequences IS26 and ISAba125, which appeared interrupted by IS5. The res and parA genes were found in the same orientation downstream of the IS26 element. To our knowledge, this is the first report of an NDM-7- carbapenemase carried on an IncX4 plasmid, as well as the first E. coli strain belonging to ST679 harboring an NDM β-lactamase, possibly associated with previous travel to Pakistan. In addition, this study highlights the dissemination of NDM variants accompanied by IncX-type plasmids. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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226. Characterization of the Genetic Environment of the blaVEB-4 Gene, Associated with a Transposable Region in a Proteus mirabilis Clinical Isolate.
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Espinal, Paula, Miró, Elisenda, Ramoneda, Laia, Flores, Manel, Rivera, Alba, Coll, Pere, and Navarro, Ferran
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URINARY tract infections , *NOSOCOMIAL infections , *PENICILLIN , *CEPHALOSPORINS , *AMINOGLYCOSIDES , *IMIPENEM , *QUINOLONE antibacterial agents - Abstract
Proteus mirabilis is the second most common cause of urinary tract infections and is also an important cause of nosocomial infections. TEM-type and CTX-M-type extended-spectrum β-lactamases (ESBLs) are the most widely distributed in this bacterial species, but minor ESBLs such as the VEB-type have also been identified. The aim of this study was to analyze the genetic environment of the blaVEB-4 gene found in a P. mirabilis clinical isolate recovered in Spain. P. mirabilis N2231 showed resistance to penicillins, cephalosporins, and aminoglycosides, remaining susceptible to imipenem, cefoxitin, β-lactamases inhibitors, and quinolones. Southern blot analysis revealed that blaVEB-4 was located in the chromosome. Analysis of the blaVEB-4 genetic context revealed a 15 kb segment 98% identical to the multidrug resistance (MDR) region of a Salmonella genomic island 1 (SGI1), which included a class 1 integron belonging to the In104 family, previously described in blaVEB-6-producing P. mirabilis VB1248. blaVEB-4 was surrounded by repeat elements, transposon Tn 1721, and located on a class 1 integron containing aacA4-aadB-dfrA1-orfC genes. The blaVEB-4 gene was inserted in a complex structure of a class 1 integron, which is part of an MDR region of an SGI1, possibly involved in the mobilization of the gene and homologous recombination. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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227. Identification of Trypanosoma cruzi Discrete Typing Units (DTUs) in Latin-American migrants in Barcelona (Spain).
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Abras, Alba, Gállego, Montserrat, Muñoz, Carmen, Juiz, Natalia A, Ramírez, Juan Carlos, Cura, Carolina I, Tebar, Silvia, Fernández-Arévalo, Anna, Pinazo, María-Jesús, de la Torre, Leonardo, Posada, Elizabeth, Navarro, Ferran, Espinal, Paula, Ballart, Cristina, Portús, Montserrat, Gascón, Joaquim, and Schijman, Alejandro G
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CHAGAS' disease , *TRYPANOSOMA cruzi , *GENOTYPES , *KINETOPLASTIDA , *BLOOD sampling , *GENETICS - Abstract
Trypanosoma cruzi , the causative agent of Chagas disease, is divided into six Discrete Typing Units (DTUs): TcI–TcVI. We aimed to identify T. cruzi DTUs in Latin-American migrants in the Barcelona area (Spain) and to assess different molecular typing approaches for the characterization of T. cruzi genotypes. Seventy-five peripheral blood samples were analyzed by two real-time PCR methods (qPCR) based on satellite DNA (SatDNA) and kinetoplastid DNA (kDNA). The 20 samples testing positive in both methods, all belonging to Bolivian individuals, were submitted to DTU characterization using two PCR-based flowcharts: multiplex qPCR using TaqMan probes (MTq-PCR), and conventional PCR. These samples were also studied by sequencing the SatDNA and classified as type I (TcI/III), type II (TcII/IV) and type I/II hybrid (TcV/VI). Ten out of the 20 samples gave positive results in the flowcharts: TcV (5 samples), TcII/V/VI (3) and mixed infections by TcV plus TcII (1) and TcV plus TcII/VI (1). By SatDNA sequencing, we classified the 20 samples, 19 as type I/II and one as type I. The most frequent DTU identified by both flowcharts, and suggested by SatDNA sequencing in the remaining samples with low parasitic loads, TcV, is common in Bolivia and predominant in peripheral blood. The mixed infection by TcV–TcII was detected for the first time simultaneously in Bolivian migrants. PCR-based flowcharts are very useful to characterize DTUs during acute infection. SatDNA sequence analysis cannot discriminate T. cruzi populations at the level of a single DTU but it enabled us to increase the number of characterized cases in chronically infected patients. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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228. Consideraciones sobre los comentarios a las recomendaciones del Comité Español del Antibiograma (COESANT) para la realización de los informes de sensibilidad antibiótica acumulada
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Navarro, Ferran, Oliver, Antonio, and Larrosa, María Nieves
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229. Molecular characterisation of acquired and overproduced chromosomal blaAmpC in Escherichia coli clinical isolates.
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Alonso, Noemí, Miró, Elisenda, Pascual, Vanesa, Rivera, Alba, Simó, Maria, Garcia, Maria Consol, Xercavins, Mariona, Morera, Maria Antonia, Espejo, Elena, Gurguí, Mercè, Pérez, Josefa, Rodríguez-Carballeira, Mònica, Garau, Javier, Calbo, Esther, Navarro, Ferran, Mirelis, Beatriz, and Coll, Pere
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ESCHERICHIA coli , *PLASMIDS , *GENETIC overexpression , *POLYMERASE chain reaction , *REPLICONS - Abstract
Escherichia coli recovered from three hospitals in Barcelona (Spain) were studied to determine the prevalence of isolates with acquired AmpC (ac-AmpC) and/or overproduced chromosomal AmpC (c-AmpC). Mechanisms involved in bla c-AmpC overexpression, bla ac-AmpC and the plasmids associated with their distribution as well as the prevalence of plasmid-mediated quinolone resistance (PMQR) in AmpC-producing isolates were also determined. Isolates were selected according to their resistance phenotype. bla ac-AmpC , alterations in the bla c-AmpC promoter/attenuator, and PMQR genes [ qnrA , qnrB , qnrS , aac(6′)-Ib -cr and qepA ] were characterised by PCR and sequencing. bla c-AmpC expression was determined by qRT-PCR. Population structure analysis was performed using PFGE, MLST and phylogenetic group PCR. Plasmids carrying bla ac-AmpC were characterised by PCR-based replicon typing and S1-PFGE. IncI1 and IncF plasmids were also analysed by plasmid MLST and replicon sequence typing, respectively. Among 21 563 E. coli isolates, 240 (1.1%) overproduced AmpC β-lactamases, including 180 (75.0%) harbouring ac-AmpC (132 CMY-2 variants and 48 DHA-1) and 60 (25.0%) c-AmpC enzymes. Three mutation profiles in the bla c-AmpC promoter/attenuator were associated with a 72.5-, 19.9- and 5.8-fold increased expression, respectively. Moreover, 63.3% of ac-AmpC and 43.3% of c-AmpC isolates belonged to B2, D, E or F phylogenetic groups. PMQR was found in 31% of ac-AmpC isolates [38 qnrB4 , 8 aac(6′)-Ib -cr, 6 qnrS1 and 3 qnrB19 ] and in 10% of c-AmpC isolates [5 aac(6′)-Ib -cr and 1 qnrS1 ]. IncI1-ST12 and IncF were associated with bla CMY-2 and bla DHA-1 , respectively. These results suggest that ac-AmpC β-lactamases were the main mechanism of AmpC production. Isolates and plasmids both showed high genetic diversity. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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230. Viral culture and immunofluorescence for the detection of SARS-CoV-2 infectivity in RT-PCR positive respiratory samples.
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Berengua, Carla, López, Marina, Esteban, Montserrat, Marín, Pilar, Ramos, Paula, Cuerpo, Margarita del, Gich, Ignasi, Navarro, Ferran, Miró, Elisenda, and Rabella, Núria
- Abstract
• Viral isolation was successful in 58% of respiratory samples with positive RT-PCR. • SARS-CoV-2 isolation is correlated with days of symptoms and RT-PCR Ct value. • SARS-CoV-2 infectivity lasts no more than 14 days in immunocompetent individuals. • Ct value <22 always indicates infectivity. Knowing how long SARS-CoV-2-positive individuals can remain infective is crucial for the design of infection prevention and control strategies. Viral culture is the gold standard for detecting an active-replicative virus and evaluating its infectious potential. To assess the correlation of SARS-CoV-2 infectivity with the number of days from symptom onset and the Ct value, using culture as a reference method. Also, to describe a detailed protocol for SARS-CoV-2 culture and immunofluorescence confirmation based on our experience with other respiratory viruses. 100 consecutive respiratory samples positive for SARS-CoV-2 by RT-PCR from different subjects were inoculated into VERO E6 cells. Viral isolation was successful in 58% of samples. The median number of days from symptom onset for culture-positive samples was 2, and 15 for culture-negative samples. Six positive cultures were obtained in patients ≥14 days after symptom onset, all of whom were immunocompromised or with severe COVID-19. The mean Ct value was 12.64 units higher in culture-negative than in culture-positive samples. The probability of successfully isolating SARS-CoV-2 in samples with a Ct value <22 was 100%, decreasing to 3.1% when >27. Our findings show a significant positive correlation between the probability of isolating SARS-CoV-2 in culture, fewer days of symptoms and a lower RT-PCR Ct value. SARS-CoV-2 infectivity lasts no more than 14 days from symptom onset in immunocompetent individuals. In contrast, in immunocompromised patients or those with severe COVID-19 infectivity may remain after 14 days. Ct value <22 always indicates infectivity. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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231. Molecular identification of aminoglycoside-modifying enzymes in clinical isolates of Escherichia coli resistant to amoxicillin/clavulanic acid isolated in Spain.
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Fernández-Martínez, Marta, Miró, Elisenda, Ortega, Adriana, Bou, Germán, González-López, Juan José, Oliver, Antonio, Pascual, Alvaro, Cercenado, Emilia, Oteo, Jesús, Martínez-Martínez, Luis, and Navarro, Ferran
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AMINOGLYCOSIDES , *BACTERIAL enzymes , *ESCHERICHIA coli , *AMOXICILLIN , *CLAVULANIC acid - Abstract
The activity of eight aminoglycosides (amikacin, apramycin, arbekacin, gentamicin, kanamycin, neomycin, netilmicin and tobramycin) against a collection of 257 amoxicillin/clavulanic acid (AMC)-resistant Escherichia coli isolates was determined by microdilution. Aminoglycoside resistance rates, the prevalence of aminoglycoside-modifying enzyme (AME) genes, the relationship between AME gene detection and resistance phenotype to aminoglycosides, and the association of AME genes with mechanisms of AMC resistance in E. coli isolates in Spain were investigated. Aminoglycoside-resistant isolates were screened for the presence of genes encoding common AMEs [ aac(3)-Ia , aac(3)-IIa , aac(3)-IVa , aac(6 ′ )-Ib , ant(2 ″ )-Ia , ant(4 ′ )-IIa and aph(3 ′ )-Ia ] or 16S rRNA methylases ( armA , rmtB , rmtC and npmA ). In total, 105 isolates (40.9%) were resistant to at least one of the aminoglycosides tested. Amikacin, apramycin and arbekacin showed better activity, with MIC 90 values of 2 mg/L (arbekacin) and 8 mg/L (amikacin and apramycin). Kanamycin presented the highest MIC 90 (128 mg/L). The most common AME gene was aac(6 ′ )-Ib (36 strains; 34.3%), followed by aph(3 ′ )-Ia (31 strains; 29.5%), ant(2 ″ )-Ia (29 strains; 27.6%) and aac(3)-IIa (23 strains; 21.9%). aac(3)-Ia , aac(3)-IVa , ant(4 ′ )-IIa and the four methylases were not detected. The ant(2 ″ )-Ia gene was usually associated with OXA-1 [21/30; 70%], whilst 23/25 (92%) strains producing CTX-M-15 had the aac(6 ′ )-Ib gene. The most prevalent AME gene was aac(6 ′ )-Ib (18/41; 44%) in nosocomial isolates, whilst ant(2 ″ )-Ia and aph(3 ′ )-Ia genes (20/64; 31%) were more frequent in strains of community origin. In 64.6% isolates the phenotypic profile correlated with the presence of commonly encountered AMEs. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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232. Epidemiology and risk factors for infections due to AmpC β-lactamase-producing Escherichia coli.
- Author
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Pascual, Vanesa, Ortiz, Gabriel, Simó, Maria, Alonso, Noemí, Garcia, Maria Consol, Xercavins, Mariona, Rivera, Alba, Morera, Maria Antonia, Miró, Elisenda, Espejo, Elena, Navarro, Ferran, Gurguí, Mercè, Pérez, Josefa, Rodríguez-Carballeira, Mónica, Garau, Javier, and Calbo, Esther
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BETA lactamases , *AMIDASES , *ESCHERICHIA coli , *ESCHERICHIA , *COLIFORMS - Abstract
Objectives To describe the prevalence and risk factors for infection due to AmpC β-lactamase-producing Escherichia coli (AmpC-EC). Methods For the prevalence study, all clinical isolates of E. coli with reduced susceptibility to third-generation cephalosporins were prospectively included from June 2010 to November 2011. For risk factor analysis, a case–control study was conducted. Cases were patients with an infection due to AmpC-EC. Controls were patients infected with cephalosporin-susceptible E. coli, matched 1 : 2. Detection of blaAmpC genes was done with a multiplex AmpC–PCR, and hyperproduction of E. coli chromosomal blaAmpC by quantitative RT–PCR. Alteration of the blaAmpC promoter was studied by PCR and sequencing. Results We identified 243 (1.1%) AmpC-EC strains out of 21 563 clinical isolates. Three cases with strains carrying ESBLs, 18 strains that were considered due to colonization and 8 cases lost to clinical follow-up were excluded. Finally, 214 cases were included in the analysis. Ninety-one cases (42.5%) and 269 (62.8%) controls were strictly community acquired (P < 0.001). Thirty-five (16.3%) cases and 186 controls (43.5%) did not have any identifiable risk factor (P < 0.001). Among cases, 158 (73.8%) were found to harbour an acquired AmpC (73.4% CMY-2). Previous use of fluoroquinolones [OR 2.6 (95% CI 1.12–3.36); P = 0.008] was independently associated with AmpC-EC in the multivariate analysis. Conclusions Prevalence of AmpC in E. coli remains low in our area. Plasmid acquisition (CMY type) represents the main mechanism of AmpC production. A high proportion of community-acquired isolates and patients with no identifiable risk factors were found. Previous use of fluoroquinolones was identified as a risk factor. [ABSTRACT FROM PUBLISHER]
- Published
- 2015
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233. Plasmid typing and genetic context of AmpC β-lactamases in Enterobacteriaceae lacking inducible chromosomal ampC genes: findings from a Spanish hospital 1999–2007.
- Author
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Mata, Caterina, Miró, Elisenda, Alvarado, Andrés, Garcillán-Barcia, M. Pilar, Toleman, Mark, Walsh, Timothy R., de la Cruz, Fernando, and Navarro, Ferran
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PLASMID genetics , *BETA lactamases , *ENTEROBACTERIACEAE , *MOBILE genetic elements , *TRANSPOSONS - Abstract
Objectives To gain insights into ampC transmission between bacterial strains. Methods We examined the genetic context of 117 acquired ampC genes from 27119 Enterobacteriaceae collected between 1999 and 2007. Plasmid analysis was carried out by PCR-based replicon or relaxase typing, S1-PFGE and Southern hybridization. I-CeuI/PFGE was used for isolates not characterized by plasmid analysis. PCR reactions were used to map the genetic organization of the ampC genes. Results Among the isolates studied, 81.2% of ampC genes were located on plasmids of known Inc/MOB groups, 7.7% were chromosomally located and 11.1% were not determined. A/C, I1 and K were the most commonly found replicons in plasmids carrying blaCMY-2, while L/M replicons were associated with blaDHA-1. blaACC-1 was linked to I1 and MOBF11 plasmids; blaCMY-27 was associated with IncF and MOBP12 plasmids; the plasmid carrying blaCMY-25 could not be typed, and blaCMY-40 was chromosomally located. All 87 isolates carrying blaCMY-2, blaCMY-4, blaCMY-25, blaCMY-27, blaCMY-40 or blaACC-1 displayed the transposon-like structures ISEcp1/ΔISEcp1-blaCMY-blc-sugE or ΔISEcp1-blaACC-1-gdha. The most prevalent structure in blaDHA-1 (93.3% of cases) was identical to that described in the Klebsiella pneumoniae pTN60013 plasmid. Remarkably, in three isolates containing chromosomal blaCMY-2, this gene was mobilized by conjugation. Conclusions Although plasmids are the main cause of the rapid dissemination of ampC genes among bacteria, we need to be aware that other mobile genetic elements such as integrative and conjugative elements (ICEs) can be involved in the mobilization of these genes. [ABSTRACT FROM PUBLISHER]
- Published
- 2012
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234. Cephalosporin-resistant Escherichia coli among summer camp attendees with salmonellosis.
- Author
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Prats, Guillem, Mirelis, Beatriz, Miro, Elisenda, Navarro, Ferran, Llovet, Teresa, Johnson, James R., Camps, Neus, Dominguez, Angela, Salleras, Lluis, Miró, Elisenda, Domínguez, Angela, and Salleras, Lluís
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FOOD poisoning , *SALMONELLA , *GASTROENTERITIS , *GASTROINTESTINAL diseases , *PLASMIDS - Abstract
Investigation of an acute gastroenteritis outbreak involving >100 persons at a summer camp in Girona, Spain, in June 2002 led to the detection of Salmonella enterica and extended-spectrum cephalosporin-resistant Escherichia coil (ESCREC). Stool cultures were performed for 22 symptomatic campers, three asymptomatic food handlers, and 10 healthy household members. Of the 22 campers, 19 had Salmonella enterica, 9 had an ESCREC strain carrying an extended-spectrum β-lactamase, and 2 had a second ESCREC strain carrying a plasmidic cephamycinase. Related ESCREC were detected in two (salmonella-negative) asymptomatic food handlers and in none of the healthy household members. Fecal ESCREC and its β-lactamases and plasmids were extensively characterized. Three of the five ESCREC clones were recovered from multiple hosts. The apparent dissemination of ESCREC suggests a food or water vehicle. The observed distribution of resistance plasmids and β-lactamase genes in several clones indicates a high degree of horizontal transfer. Heightened vigilance and increased efforts must be made to discover the reservoirs and vehicles for community dissemination of ESCREC. [ABSTRACT FROM AUTHOR]
- Published
- 2003
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235. GASVeM: A New Machine Learning Methodology for Multi-SNP Analysis of GWAS Data Based on Genetic Algorithms and Support Vector Machines.
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Díez Díaz, Fidel, Sánchez Lasheras, Fernando, Moreno, Víctor, Moratalla-Navarro, Ferran, Molina de la Torre, Antonio José, Martín Sánchez, Vicente, and Rho, Seungmin
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SUPPORT vector machines , *GENETIC algorithms , *MACHINE learning , *COLORECTAL cancer , *DATABASES , *DATA analysis - Abstract
Genome-wide association studies (GWAS) are observational studies of a large set of genetic variants in an individual's sample in order to find if any of these variants are linked to a particular trait. In the last two decades, GWAS have contributed to several new discoveries in the field of genetics. This research presents a novel methodology to which GWAS can be applied to. It is mainly based on two machine learning methodologies, genetic algorithms and support vector machines. The database employed for the study consisted of information about 370,750 single-nucleotide polymorphisms belonging to 1076 cases of colorectal cancer and 973 controls. Ten pathways with different degrees of relationship with the trait under study were tested. The results obtained showed how the proposed methodology is able to detect relevant pathways for a certain trait: in this case, colorectal cancer. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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236. Detection of three stable genetic clones of CTX-M-15-producing Klebsiella pneumoniae in the Barcelona metropolitan area, Spain.
- Author
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Coelho, Alicia, Mirelis, Beatriz, Alonso-Tarrés, Carles, Larrosa, María Nieves, Miró, Elisenda, Abad, Raquel Clivillé, Bartolomé, Rosa María, Castañer, Mireia, Prats, Guillem, Johnson, James R., Navarro, Ferran, and González-López, Juan José
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GENETIC research , *CLONING , *KLEBSIELLA pneumoniae , *NOSOCOMIAL infections , *HOSPITALS - Abstract
The article presents a study that deals with genetic clones of CTX-M-15-producing Klebsiella pneumoniae in the Barcelona metropolitan area in Spain. The authors assessed the clonality and persistence of CTX-M-15-producing K. pneumoniae isolates. A retrospective study of extended-spectrum ß-lactamases-producing K. pneumoniae clinical samples was conducted. They were collected from samples stored from 2005 through 2008 at Hospital Sant Pau and Hospital Val d'Hebron. Also included in the study were all the ESBL-producing K. pneumoniae isolates encountered at Hospital General de l'Hospitalet during the outbreak period in July 2008. Based on their findings, the authors highlighted the dissemination and persistence of three K. pneumoniae clonal strains producing CTX-M-15.
- Published
- 2009
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237. Serveis a les platges per als usuaris dels dispositius electrònics de mà
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Abellán Cardona, Joaquín, Universitat Politècnica de Catalunya. Departament d'Enginyeria de Projectes i de la Construcció, González Benítez, María Margarita, and López Navarro, Ferran
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Bags ,Personal paraphernalia -- Conservation and restoration ,Enginyeria dels materials::Materials plàstics i polímers [Àrees temàtiques de la UPC] ,Objectes personals -- Conservació i restauració ,Bosses - Published
- 2016
238. Millora del disseny d’un armari d’aigua potable
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Pont Ribas, Xavier, Universitat Politècnica de Catalunya. Departament de Projectes d'Enginyeria, López Navarro, Ferran, Puig Oliveras, Oriol, and González Benítez, María Margarita
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Water -- Purification ,Enginyeria civil::Enginyeria hidràulica, marítima i sanitària [Àrees temàtiques de la UPC] ,Aigua -- Depuració -- Mètodes ,Maquinaria -- Disseny - Published
- 2016
239. Rediseño de la boca de aspiración instalada en las paredes de una piscina mediante la metodología del análisis de valor
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Valenzuela Cuesta, Eloi, Universitat Politècnica de Catalunya. Departament de Projectes d'Enginyeria, Fernández Seijas, Jorge, and López Navarro, Ferran
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Enginyeria química::Química del medi ambient [Àrees temàtiques de la UPC] ,Water -- Purification ,Aigua -- Depuració ,Filtres i filtració - Abstract
Actualmente, la sociedad vive una constante evolución donde el diseño de un mismo producto se va reinventando con tal de ofrecer un mejor servicio a sus clientes y un proceso de fabricación cada vez más óptimo. De esta manera, el objeto del presente proyecto es analizar la posibilidad de llevar a cabo un rediseño de la boca de aspiración instalada en las paredes de las piscinas perteneciente a la empresa METALAST SAU, del grupo Fluidra, empleando la metodología del análisis de valor. A este elemento se le denomina skimmer, y tiene como función principal aspirar la lámina de agua para su filtración y tratamiento. Se analizaran todos los campos que intervienen en su proceso de diseño y fabricación con tal de presentar una nueva propuesta que optimice la relación función/coste. Utilizando la técnica de análisis de valor se va a rediseñar este elemento de manera que manteniendo sus funcionalidades se van a reducir sus costes de manufactura, ensamblaje y mantenimiento.
- Published
- 2016
240. Epidemiologia de la carbapenemasa OXA-48 en aïllats de Klebsiella pneumoniae a Catalunya
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Argente Viñals, Marc, Navarro, Ferran, Miró, Elisenda, and Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia
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Ciències Experimentals ,Carbapenemasa ,Klebsiella ,Carbepenemase ,OXA-48 - Abstract
La carbapenemasa OXA-48 esta àmpliament estesa arreu del món i principalment en Enterobacteriaceae. A Catalunya, Klebsiella pneumoniae productora de la carbapenemasa OXA-48 es va detectar per primer cop al 2009, i des d’aleshores semblava observar-se un cert increment. L’observació d’aquest increment per part de diferents hospitals fou la raó per a iniciar aquest estudi multicèntric que inclou 11 hospitals comarcals i l’Hospital de la Santa Creu i Sant Pau i que té com a principal objectiu la caracterització, tant a nivell epidemiològic com molecular, de les soques de K. pneumoniae productores d’OXA-48 aïllades al llarg del 2012. En l’estudi es van incloure totes aquelles soques de K. pneumoniae que presentaven un fenotip de resistència als antibiòtics betalactàmics diferent al patró natural esperat. A les soques seleccionades se’ls hi va realitzar el test de Hodge modificat (THM) per poder evidenciar la presència de qualsevol enzim amb activitat enfront els carbapenèmics. D’un total de 3.901 soques de K. pneumoniae aïllades, 171 (4,4%) van ser positives per al THM. Per PCR es van confirmar com a portadores de l’OXA-48 85 soques (49,7%). El vuitanta nou percent de les 85 soques productores de l’OXA-48 coexpressaven la BLEA CTX-M-15, acompanyada o no d’OXA-1 i/o TEM-1. Es va estudiar la clonalitat d’aquestes 85 soques per macrorestricció genòmica (PFGE) i MultiLocus Sequencing Type (MLST). Per PFGE es varen observar cinc clones: A, B, C, D i E; que es van correlacionar perfectament amb les cinc seqüència tipus trobades: ST101, ST17, ST1233, ST14 i ST405. La ST1233 va ser descrita per primer cop en aquest estudi. El gen blaOXA-48 es trobat situat en un plasmidi conjugatiu del grup d’incompatibilitat IncL, (62 Kb aprox) i localitzat majoritàriament en Tn1999.2 (91,7%). Es va descartar que la resta de betalactamases trobades estiguessin en aquest plasmidi. De les 85 soques productores d’OXA-48, 75 (88,23%) tenien el gen qnrB. També es varen estudiar els gens implicats en la resistència enzimàtica als aminoglicòsids. De les 85 soques estudiades, 82 es mostraren resistents a algun dels aminoglicòsid estudiats, El fenotip majoritari, va ser la resistència a kanamicina, tobramicina i gentamicina (KTG) i s’explica per la presència dels gens aac(3’)-IIa (KTGN) i aac(6)-Ib (KTAN). Es van observat que soques genèticament relacionades (igual PFGE, ST i presencia dels mateixos gens de resistència) presentaven nivells de resistència diferents. Aquestes diferencies no es varen poder associar a l’activació de bombes d’expulsió AcrAB ni alteracions de les porines estudiades. Els resultats obtinguts per les tècniques clàssiques (PCR, Seqüenciació, PFGE i MLST) van ser comparats en 37 soques amb la nova tècnica de la seqüenciació massiva del genoma microbià (Whole Genome Sequencing: WGS) i el cgMLST (core genome MultiLocus Sequence Typing). Es resultats mostraren una bona correlació entre PFGE-MLST i cgMLST. A l’introduir les seqüències obtingudes pel WGS als webs PlasmidFinder i al ResFinder, vàrem poder identificar plasmidis recentment tipificats i la presència d’altres gens de resistència, com: strA/strB, oqxA/oqxB ,drfA, sul2, fosA, catB3, tet(A) i tet(D). Amb les seqüències obtingudes per WGS també es va obtenir les seqüències de les dianes d’acció de les quinolones, els QRDR. Nomes es varen detectar alteracions en les tres soques del ST101. En conclusió, l’increment de la prevalença de K. pneumoniae portadora d’OXA-48 a Catalunya es deu a la presència en tots els hospitals on s’han aïllat aquestes soques de l’expansió de les clones ST405 i ST101. No havent-hi trobat diferencies en l’entorn genètic del gen que es el mateix que s’ha anat a descrivint arreu. Per altra banda, podem afirmar que la WGS és una bona eina per a la descripció epidemiològica i molecular de brots produïts per a soques multiresistents., The OXA-48 carbapenemase is widely spread around the world and found mainly in Enterobacteriaceae. In Catalonia, OXA-48-producing Klebsiella pneumoniae was first detected in 2009, since then, a growing prevalence has been observed in different hospitals, which prompted the aim of this multicenter study, which includes 11 regional hospitals and the Hospital de Santa Creu i Sant Pau, is the characterization, both epidemiological and molecular, of OXA-48–producing K. pneumoniae strains isolated throughout 2012. The study included all K. pneumoniae strains with an unusual pattern of resistance to beta-lactam antibiotics. Selected strains underwent a modified Hodge test (MHT) to detect any enzyme activity against carbapenemics. A total of 3,901 K. pneumoniae strains, 171 MHT-positive strains (4.4%) were selected. PCR confirmed that 85 strains carried OXA-48 (49.7%). Eighty nine percent of the 85 OXA-48–producing strains coexpressed the ESBL CTX-M-15, with or without beta-lactamases OXA-1 and TEM-1. The clonality of these 85 OXA-48–producing strains was studied by macrorestriction analysis (PFGE) and multilocus sequence typing (MLST). Five clones were observed by PFGE: A, B, C, D and E. These five clones were perfectly correlated with the five sequence types found, ST101, ST17I, ST1233, ST14 and ST405. ST1233 is described for the first time in this study. The blaOXA-48 gene was found in a conjugative plasmid of incompatibility group IncL (aprox. 62 Kb) and located in Tn1999.2 (91.7%). The other beta-lactamase genes of these strains were not found in this plasmid. Of the 85 OXA-48–producing strains, 75 (88.23%) harboured the qnrB gene. Genes involved in enzyme-mediated resistance against aminoglycosides were also studied. Of the 85 OXA-48–producing strains, 82 showed resistance to some of the aminoglycosides studied. The major phenotype showed resistance to kanamycin, gentamicin and tobramycin (KTG), and it was explained by the presence of aac(3')-IIa (KTGN) and aac(6’)-Ib (KTAN) genes. We observed that genetically related strains (that is, closely related PFGE, identical ST and the presence of the same resistance genes) showed different levels of resistance. These differences couldn’t be due to alterations in the expression of the efflux pump AcrAB or in porins. Results obtained by classical techniques (PCR, sequencing, PFGE and MLST) in 37 strains selected were compared with those of the new techniques of massive sequencing of microbial genomes (Whole Genome Sequencing: WGS) and cgMLST (core genome MultiLocus Sequence Typing). A good correlation was found between PFGE-MLST and cgMLST, and four strains were identical by cgMLST but not by PFGE. After uploading the sequences obtained by WGS to the PlasmidFinder and ResFinder online search tools, we were able to identify recently classified plasmids and determine the presence of other resistance genes, such as: strA / strB, oqxA / oqxB, drfA, sul2, fosA, catB3, tet(A) and tet(D). The use of WGS allowed us to obtain sequences of the targets of the quinolones, the QRDR. Surprisingly, only alterations described as responsible for this resistance were detected in all three ST101 strains. In conclusion, the increase in the prevalence of OXA-48-carrying K. pneumoniae in Catalonia is due to the expansion of the ST405 and ST101 clones in all hospitals where strains were isolated. No differences in the genetic background of the blaOXA-48 gene were found, as reported elsewhere. Moreover, WGS was found to be a useful tool for the molecular and epidemiological analysis of outbreaks caused by multidrug-resistant strains.
- Published
- 2016
241. Modelización gráfica y simulación de un motor Stirling
- Author
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Carroggio Cabestany, Alberto, López Navarro, Ferran, and Universitat Politècnica de Catalunya. Departament de Projectes d'Enginyeria
- Subjects
Motors Stirling -- Simulació per ordinador ,Motors Stirling -- Models matemàtics ,Stirling engines -- Mathematical models ,Stirling engines -- Computer simulation ,Enginyeria mecànica::Motors [Àrees temàtiques de la UPC] - Abstract
El siguiente trabajo presenta primeramente a los motores Stirling, realizando una breve explicación de su funcionamiento y características. Una vez conocidos, se centra en los motores Stirling con configuración Alfa. Se establece un proceso de diseño de motores Stirling tipo Alfa con el que poder hacer frente a cálculos matemáticos que ayudan a conocer las características del motor diseñado antes de su fabricación. Se realizan un estudio térmico y cinemático de forma que se conozcan las variables que afectan al funcionamiento del motor y que serán objeto de estudio a la hora del diseño. Esto sirve para así obtener relaciones entre variables térmicas y cinemáticas con las que poder establecer los cálculos que condicionarán el diseño del motor. Una vez realizado un primer cálculo, se realiza un proceso de optimización mediante el estudio de los cálculos obtenidos al modificar alguna de las variables más expuestas a ser objeto de cambio, como son la presión o el ángulo de desfase entre pistones. Lo citado anteriormente se realiza primeramente con carácter general, sin embargo se realiza posteriormente el diseño de un motor, con característica de funcionamiento especificadas por el autor, a modo de prueba. Esto se realiza con el fin de valorar los cálculos realizados y el proceso de diseño. Finalmente se realiza el diseño en soporte CAD con el que poder realizar pruebas de movimiento del motor diseñado, ver variaciones de volumen, realizar planos y demás características cinemáticas del motor objeto de diseño propuesto.
- Published
- 2015
242. Millora i redisseny del procés de fabricació i muntatge d’un pilot per automoció
- Author
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Miravall Méndez, Gerard, López Navarro, Ferran, González Benítez, María Margarita, and Universitat Politècnica de Catalunya. Departament de Projectes d'Enginyeria
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Automobiles -- Electronic equipment -- Quality control ,Automòbils -- Equipament electrònic -- Control de qualitat ,Enginyeria mecànica::Disseny i construcció de vehicles [Àrees temàtiques de la UPC] ,Automobiles -- Electronic equipment -- Disseny ,Automòbils -- Equipament electrònic -- Disseny ,Enginyeria electrònica::Microelectrònica [Àrees temàtiques de la UPC] - Abstract
Aquest projecte estudia els problemes de qualitat que sorgeixen en una planta fabricació de pilots per automoció, concretament el problema en l’allotjament del casquet que uneix el pilot posterior amb la carrosseria de l’actual Volkswagen Polo. Per solucionar-lo, es proposa una millora funcional per canviar el sistema d’unió entre l’allotjament del casquet en el cos del pilot i el casquet. Es segueix un camí basat en la prova-error, que integra càlculs i simulacions, per arribar a una solució final.
- Published
- 2015
243. Disseny i estudi de les sol·licitacions d’un seient de tren mitjançant CATIA V5
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Ajates Temprana, Guillem, Universitat Politècnica de Catalunya. Departament de Projectes d'Enginyeria, and López Navarro, Ferran
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Enginyeria mecànica::Disseny i construcció de vehicles::Ferrocarrils [Àrees temàtiques de la UPC] ,Ferrocarrils -- Disseny i construcció ,Railroads --Design and construction - Abstract
El present estudi té l’objectiu de dissenyar un seient de tren individual que compleixi els requeriments estructurals i ergonòmics de diverses normatives europees i americanes a partir de les eines CAD/CAE adequades (Catia V5 i PamCrash). Per a la consecució d’aquest objectiu, s’ha partit del model Metropolis de l’empresa especialitzada en la fabricació de seients per a vehicles industrials, Fainsa. Mitjançant l’enginyeria inversa, s’ha realitzat el disseny bàsic d’aquest seient. Paral·lelament, s’ha fet un estudi de la normativa europea i americana, a partir de les quals s’han redactat els plecs de condicions estructurals i ergonòmiques. A partir de la geometria obtinguda, s’han realitzat les simulacions dels assajos i s’han dut a terme diferents modificacions estructurals (afegint un nervi posterior i costelles internes) per tal de millorar aquests resultats i optimitzar el disseny. Les simulacions dels diferents assajos es realitzen amb Catia V5, juntament amb el software PamCrash. En funció dels resultats obtinguts en cadascun dels models, s’ha escollit la millor opció. Finalment, s’ha realitzat un estudi del impacte ambiental del disseny realitzat i una avaluació econòmica de les diferents fases del projecte. En aquest estudi, també s’inclouen annexos amb informació addicional sobre els punts tractats, com el disseny pas a pas del seient, una explicació detallada dels càlculs realitzats, catàlegs de materials, plànols, etc.
- Published
- 2012
244. Concepció i desenvolupament d'una carrosseria per un vehicle de la Formula Student
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Carrillo Ruiz, Daniel, López Navarro, Ferran, and Universitat Politècnica de Catalunya. Departament de Projectes d'Enginyeria
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Automobiles, Racing -- Bodies -- Design and construction ,Enginyeria mecànica::Disseny i construcció de vehicles::Automòbils [Àrees temàtiques de la UPC] ,Automòbils de competició -- Carrosseries -- Projectes i construcció - Abstract
Premi al millor Projecte de Fi de Carrera presentat durant l'any 2012 en l'àmbit d'Automoció que atorga la CÀTEDRA SEAT-UPC. El present document tracta del disseny i fabricació d'una carrosseria no estructural per al monoplaça CAT03 de l'equip ETSEIB Motorsport, en el marc de la Formula Student. Es desenvolupa el disseny conceptual, d'estil, el projectat, es realitzen els càlculs necessaris per la seva validació i posteriorment es fabrica la carrosseria amb fibra de carboni i fibra de vidre. El projecte representa una formació complementària als estudis d'Enginyeria Industrial a l'Escola Tècnica Superior d'Enginyeria Industrial de Barcelona i correspon a la tercera participació de l'equip en la competició (temporada 2010). El monoplaça ha competit a Alemanya (Hockenheim), Itàlia (Varano) i Catalunya (Montmeló). Està estructurat per àrees temàtiques i l’ordre dels capítols manté una certa relació amb la seqüència cronològica de les diferents fases de disseny i fabricació. Els primers capítols presenten la carrosseria com a concepte, es planteja la normativa aplicable i les normes de competició. Es realitza un anàlisi d'usuaris, funcions i alternatives. La memòria tècnica mostra com es resolen els diferents sistemes de la carrosseria, les línies de caràcter, les superfícies d'estil, es projecta la carrosseria i es decideix la tipologia de material compost a utilitzar. Es mostra els càlculs bàsics d'aerodinàmica i càlculs d'esforç i la resolució del disseny final. Es tracta el disseny i fabricació dels motllos amb els que fabricar la carrosseria i les últimes accions per integrar-ho al monoplaça. Per últim s'explica quin hauria de ser el treball d'edicions posteriors per l'equip ETSEIB Motorsport, l'estudi econòmic i a quins pactes s'arriben amb els espònsors, l'estimació de l'impacte ambiental del projecte i la planificació temporal del departament encarregat de confeccionar la carrosseria. Award-winning
- Published
- 2012
245. Reducción de variantes de elementos de fijación en modelos SEAT
- Author
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Rodríguez García, Alejandro, Universitat Politècnica de Catalunya. Departament de Projectes d'Enginyeria, Miguel Pérez, Javier de, and López Navarro, Ferran
- Subjects
Automobiles -- Equipment and supplies ,Automòbils -- Equip i accessoris ,Enginyeria mecànica::Disseny i construcció de vehicles::Automòbils [Àrees temàtiques de la UPC] ,Automobiles -- Manufacturing processes ,Automòbils -- Fabricació - Abstract
En el presente proyecto final de carrera se muestran los procedimientos que se han llevado a cabo para promover una reducción de variantes de elementos de fijación en las piezas de acabados internos de los modelos Seat. Gran parte del procedimiento se centra en un tipo de clip que suma aproximadamente el 50% del total de fijaciones que aparece en los revestimientos internos. Dada la gran importancia de este tipo de fijación en el área, su estudio se convierte en una necesidad para poder conocer de primera mano las variables del entorno que afectan a su correcto funcionamiento. Para ello, se han analizado estadísticamente los resultados experimentales que se habían llevado a cabo previamente con el objetivo de encontrar el único elemento que mejor se adaptase a un conjunto de situaciones y poder modelar su entorno a través de expresiones matemáticas. Asimismo, en este proyecto se analizan económicamente las consecuencias de promover dicha reducción de variantes, que además proporciona ventajas y facilidades a los operarios de la línea de montaje, permitiendo indirectamente una reducción en los tiempos de montaje. En líneas de reducción y simplificación, se ha optimizado el diseño de un componente utilizado frecuentemente en acabados internos para facilitar al proyectista el desarrollo de este elemento en un tiempo altamente reducido.
246. Bacteriuria and phenotypic antimicrobial susceptibility testing in 45 min by point-of-care Sysmex PA-100 System: first clinical evaluation.
- Author
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Alonso-Tarrés C, Benjumea Moreno C, Navarro F, Habison AC, Gonzàlez-Bertran E, Blanco F, Borràs J, Garrigó M, and Saker J
- Subjects
- Humans, Female, Sensitivity and Specificity, Bacteria drug effects, Bacteria isolation & purification, Point-of-Care Systems, Urinary Tract Infections microbiology, Urinary Tract Infections diagnosis, Urinary Tract Infections drug therapy, Adult, Middle Aged, Aged, Young Adult, Aged, 80 and over, Adolescent, Bacteriuria diagnosis, Bacteriuria microbiology, Bacteriuria drug therapy, Microbial Sensitivity Tests instrumentation, Microbial Sensitivity Tests methods, Anti-Bacterial Agents pharmacology
- Abstract
Purpose: This study compared the results of the new Sysmex PA-100 AST System, a point-of-care analyser, with routine microbiology for the detection of urinary tract infections (UTI) and performance of antimicrobial susceptibility tests (AST) directly from urine., Methods: Native urine samples from 278 female patients with suspected uncomplicated UTI were tested in the Sysmex PA-100 and with reference methods of routine microbiology: urine culture for bacteriuria and disc diffusion for AST., Results: The analyser delivered bacteriuria results in 15 min and AST results within 45 min. Sensitivity and specificity for detection of microbiologically confirmed bacteriuria were 84.0% (89/106; 95% CI: 75.6-90.4%) and 99.4% (155/156; 95% CI: 96.5-100%), respectively, for bacterial species within the analyser specifications. These are Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Enterococcus faecalis and Staphylococcus saprophyticus, which are common species causing uncomplicated UTI. Overall categorical agreement (OCA) for AST results for the five antimicrobials tested in the Sysmex PA-100 (amoxicillin/clavulanic acid, ciprofloxacin, fosfomycin, nitrofurantoin and trimethoprim) ranged from 85.4% (70/82; 95%CI: 75.9-92.2%) for ciprofloxacin to 96.4% (81/84; 95% CI: 89.9-99.3%) for trimethoprim. The Sysmex PA-100 provided an optimal treatment recommendation in 218/278 cases (78.4%), against 162/278 (58.3%) of clinical decisions., Conclusion: This first clinical evaluation of the Sysmex PA-100 in a near-patient setting demonstrated that the analyser delivers phenotypic AST results within 45 min, which could enable rapid initiation of the correct targeted treatment with no further adjustment needed. The Sysmex PA-100 has the potential to significantly reduce ineffective or unnecessary antibiotic prescription in patients with UTI symptoms., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
247. Author Correction: Titers of IgG and IgA against SARS-CoV-2 proteins and their association with symptoms in mild COVID-19 infection.
- Author
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Abril AG, Alejandre J, Mariscal A, Alserawan L, Rabella N, Roman E, Lopez-Contreras J, Navarro F, Serrano E, Nomdedeu JF, and Vidal S
- Published
- 2024
- Full Text
- View/download PDF
248. Early identification of the nosocomial spread of vancomycin-resistant Enterococcus faecium by Fourier-transform infrared spectroscopy and performance comparison with PFGE and WGS.
- Author
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Pitart C, Piquet M, Burgwinkel T, Arazo Del Pino R, Rubio M, Aguilar M, De Gea S, Pulgarín A, Campo I, Torralbo B, Parejo R, Valls S, Fortes I, Santana G, Rubio E, Vilella A, Del Río A, Martínez JA, Miró E, Navarro F, Espasa M, Casals-Pascual C, Vila J, Higgins PG, and Roca I
- Subjects
- Humans, Spectroscopy, Fourier Transform Infrared methods, Disease Outbreaks, Bacterial Proteins genetics, Microbial Sensitivity Tests, Spain epidemiology, Carbon-Oxygen Ligases genetics, Anti-Bacterial Agents pharmacology, Enterococcus faecium genetics, Enterococcus faecium drug effects, Enterococcus faecium isolation & purification, Enterococcus faecium classification, Vancomycin-Resistant Enterococci genetics, Vancomycin-Resistant Enterococci isolation & purification, Vancomycin-Resistant Enterococci drug effects, Vancomycin-Resistant Enterococci classification, Electrophoresis, Gel, Pulsed-Field, Cross Infection microbiology, Cross Infection epidemiology, Gram-Positive Bacterial Infections microbiology, Gram-Positive Bacterial Infections epidemiology, Whole Genome Sequencing methods
- Abstract
Early detection of disseminating vancomycin-resistant Enterococcus faecium (VREfm) in ICU wards is crucial for outbreak identification and the implementation of prompt infection control measures. Genotypic methods like pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) are costly and time-consuming, hindering rapid response due to batch dependency. Fourier-transform infrared spectroscopy (FT-IR) offers the potential for real-time outbreak detection and reliable strain typing. We utilized FT-IR to identify clonal VREfm dissemination and compared its performance to PFGE and WGS. Between February through October 2023, an unusually high number of VREfm were recovered at a tertiary hospital in Barcelona. Isolates were examined for antimicrobial susceptibility, carriage of vanA/vanB genes and clonality was also studied using FT-IR, PFGE, and WGS. Routine FT-IR inspections revealed recurring VREfm clustering during the outbreak's initial weeks. In total, 104 isolates were recovered from 75 patients and from multiple wards. However, only one isolate was recovered from an environmental sample, suggesting the absence of environmental reservoirs. An ST80 vancomycin-resistant ( vanA ) E. faecium strain was the main strain responsible for the outbreak, although a few additional VREfm strains were also identified, all belonging to CC17. PFGE and cgMLST (WGS) yielded identical clustering results to FT-IR, and WGS confirmed vanA/vanB gene carriage in all VREfm isolates. Infection control measures led to a rapid decline in VREfm isolates, with no isolates detected in November. FT-IR spectroscopy offers rapid turnaround times, sensitivity, and reproducibility, comparable to standard typing methods. It proved as an effective tool for monitoring VREfm dissemination and early outbreak detection.
- Published
- 2024
- Full Text
- View/download PDF
249. Titers of IgG and IgA against SARS-CoV-2 proteins and their association with symptoms in mild COVID-19 infection.
- Author
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Abril AG, Alejandre J, Mariscal A, Alserawan L, Rabella N, Roman E, Lopez-Contreras J, Navarro F, Serrano E, Nomdedeu JF, and Vidal S
- Subjects
- Humans, Male, Female, Adult, Middle Aged, Spike Glycoprotein, Coronavirus immunology, Coronavirus Nucleocapsid Proteins immunology, Immunoglobulin M blood, Immunoglobulin M immunology, Immunity, Humoral, Phosphoproteins immunology, COVID-19 immunology, COVID-19 virology, COVID-19 blood, Immunoglobulin A blood, Immunoglobulin A immunology, Immunoglobulin G blood, Immunoglobulin G immunology, SARS-CoV-2 immunology, Antibodies, Viral immunology, Antibodies, Viral blood
- Abstract
Humoral immunity in COVID-19 includes antibodies (Abs) targeting spike (S) and nucleocapsid (N) SARS-CoV-2 proteins. Antibody levels are known to correlate with disease severity, but titers are poorly reported in mild or asymptomatic cases. Here, we analyzed the titers of IgA and IgG against SARS-CoV-2 proteins in samples from 200 unvaccinated Hospital Workers (HWs) with mild COVID-19 at two time points after infection. We analyzed the relationship between Ab titers and patient characteristics, clinical features, and evolution over time. Significant differences in IgG and IgA titers against N, S1 and S2 proteins were found when samples were segregated according to time T1 after infection, seroprevalence at T1, sex and age of HWs and symptoms at infection. We found that IgM + samples had higher titers of IgG against N antigen and IgA against S1 and S2 antigens than IgM - samples. There were significant correlations between anti-S1 and S2 Abs. Interestingly, IgM + patients with dyspnea had lower titers of IgG and IgA against N, S1 and S2 than those without dyspnea. Comparing T1 and T2, we found that IgA against N, S1 and S2 but only IgG against certain Ag decreased significantly. In conclusion, an association was established between Ab titers and the development of infection symptoms., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
250. Improving the diagnosis of urinary tract infections by the use of enriched media and a 48-hour incubation period.
- Author
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Benjumea C, Navarro F, and Alonso-Tarrés C
- Subjects
- Humans, Time Factors, Bacteriological Techniques methods, Bacteriological Techniques standards, Bacteria isolation & purification, Bacteria classification, Bacteria growth & development, Agar, Urine microbiology, Urinary Tract Infections diagnosis, Urinary Tract Infections microbiology, Culture Media chemistry, Sensitivity and Specificity
- Abstract
Introduction. The absence of a gold-standard methodology for the microbiological diagnosis of urinary tract infections (UTI) has led to insufficient standardization of criteria for the interpretation of results and processing methods, particularly incubation time and culture media. Hypothesis. 48-hour incubation time period and use of blood agar enhances the sensitivity of microorganisms isolated significantly. Aim. To determine the sensitivity of blood agar and Brilliance UTI chromogenic agar, incubating for different periods (24-48 hours), for the detection of positive urine cultures. Methodoloy. Comparisons were made between all possible combinations of media and incubation times. As the gold-standard reference, we used the routine methodology of our laboratory, which involves prior screening with available clinical data, flow cytometry, sediment analysis and/or Gram staining. Screened samples were then cultured on blood agar and chromogenic agar and incubated for 48 hours. Also, based on the results of Gram staining, additional media were added in selected cases. Results. The most significant difference was found between chromogenic agar incubated for 24 hours and blood agar incubated for 48 hours, with the latter method allowing the recovery of 10.14 % more microorganisms ( P < 0.0001). Furthermore, the value of performing Gram staining to guide processing was demonstrated, as it avoided the loss of at least 5.14 % of isolates. Conclusions. At least in urological and nephrological patients it is essential to include enriched culture media (blood agar) or to extend the incubation times due to the improvement of the diagnostic sensitivity of urine cultures. Gram staining also can help detect the presence of fastidious microorganisms or mixed infections, indicating whether rich and/or selective media should be included to enhance the diagnostic sensitivity of cultures. If this methodology is not followed, it should be noted that besides fastidious species, fastidious strains of Escherichia coli, Proteus mirabilis, Pseudomonas aerugniosa and Stenotrophomonas maltophilia will also be missed.
- Published
- 2024
- Full Text
- View/download PDF
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