Search

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]

Background and Aims Genome-wide association studies [GWAS] for inflammatory bowel disease [IBD] have identified 240 risk variants. However, the benefit of understanding the genetic architecture of IBD remains to be exploited. Transcriptome-wide association studies [TWAS] associate gene expression with genetic susceptibility to disease, providing functional insight into risk loci. In this study, we integrate relevant datasets for IBD and perform a TWAS to nominate novel genes implicated in IBD genetic susceptibility. Methods We applied elastic net regression to generate gene expression prediction models for the University of Barcelona and University of Virginia RNA sequencing project [BarcUVa-Seq] and correlated expression and disease association research [CEDAR] datasets. Together with Genotype-Tissue Expression project [GTEx] data, and GWAS results from about 60 000 individuals, we employed Summary-PrediXcan and Summary-MultiXcan for single and joint analyses of TWAS results, respectively. Results BarcUVa-Seq TWAS revealed 39 novel genes whose expression in the colon is associated with IBD genetic susceptibility. They included expression markers for specific colon cell types. TWAS meta-analysis including all tissues/cell types provided 186 novel candidate susceptibility genes. Additionally, we identified 78 novel susceptibility genes whose expression is associated with IBD exclusively in immune (N = 19), epithelial (N = 25), mesenchymal (N = 22) and neural (N = 12) tissue categories. Associated genes were involved in relevant molecular pathways, including pathways related to known IBD therapeutics, such as tumour necrosis factor signalling. Conclusion These findings provide insight into tissue-specific molecular processes underlying IBD genetic susceptibility. Associated genes could be candidate targets for new therapeutics and should be prioritized in functional studies. [ABSTRACT FROM AUTHOR]

Purpose: Multimorbidity impacts quality of life. We constructed hypothyroidism comorbidity networks to identify positive and negative associations with other prevalent diseases.Methods: We analyzed data of 285 342 patients with hypothyroidism from 3 135 948 adults with multimorbidity in a population-based study in Catalonia, Spain, (period: 2006-2017). We constructed hypothyroidism comorbidity networks using logistic regression models, adjusted by age and sex, and for men and women separately. We considered relevant associations those with odds ratios (OR) >1.2 or <0.8 and P value < 1e-5 to identify coexistence greater (or smaller) than the expected by the prevalence of diseases. Multivariate models considering comorbidities were used to further adjust OR values.Results: The conditions associated included larynx cancer (adjusted OR: 2.48), congenital anomalies (2.26), thyroid cancer (2.13), hyperthyroidism (1.66), vitamin B12/folate deficiency anemia (1.57), and goiter (1.56). The network restricted to men had more connections (mental, cardiovascular, and neurological) and stronger associations with thyroid cancer (7.26 vs 2.55), congenital anomalies (5.11 vs 2.13), hyperthyroidism (4.46 vs 1.69), larynx cancer (3.55 vs 1.67), and goiter (3.94 vs 1.64). After adjustment for comorbidities, OR values were more similar in men and women. The strongest negative associations after adjusting for comorbidities were with HIV/AIDS (OR: 0.71) and tobacco abuse (0.77).Conclusions: Networks show direct and indirect hypothyroidism multimorbidity associations. The strongest connections were thyroid and larynx cancer, congenital anomalies, hyperthyroidism, anemia, and goiter. Negative associations included HIV/AIDS and tobacco abuse. The network restricted to men had more and stronger associations, but not after adjusting for comorbidities, suggesting important indirect interactions. [ABSTRACT FROM AUTHOR]

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]

Abstract: Ascitic neutrophils from cirrhotic patients with spontaneous bacterial peritonitis (SBP) exhibit an impaired oxidative burst that could facilitate bacterial infection. However, the influence of the cell‐free ascitic fluid of these patients on neutrophil function has not been investigated. To analyze this influence, we determined the ascitic levels of cytokines, resistin, and lactoferrin and their association with neutrophil function, disease severity score, and SBP resolution. We analyzed NETosis induction by microscopy and oxidative burst by the flow cytometry of healthy neutrophils cultured in ascitic fluid from cirrhotic patients with sterile ascites (SA) and with SBP before and after antibiotic treatment. Resistin, IL‐6, IL‐1 receptor antagonist, IL‐1β, and lactoferrin levels were measured in ascitic fluids and supernatants of cultured neutrophils and PBMCs by ELISA. Upon stimulation, healthy neutrophils cultured in SBP ascitic fluid produced lower NETosis and oxidative burst than those cultured in SA. Ascitic resistin levels were negatively correlated with NETosis, oxidative burst, and ascitic glucose levels; and positively correlated with the model for end‐stage liver disease score. After an E. coli or TNF‐α stimulus, neutrophils were the major resistin producers. Resistin indirectly reduced the oxidative burst of neutrophils and directly reduced the inflammatory phenotype of monocytes and TNF‐α production. Bacterial‐induced resistin production can down‐regulate the inflammatory response of macrophages and neutrophil function in ascitic fluid. Consequently, this down‐regulation may jeopardize the elimination of bacteria that translocate to ascitic fluid in patients with cirrhosis. [ABSTRACT FROM AUTHOR]

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]

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]

Objectives To characterize the vectors involved in the dissemination of blaCMY-2 genes in clinical isolates of Proteus mirabilis collected between 1999 and 2007. Methods Plasmid analysis of 19 P. mirabilis carrying ampC genes was performed by PCR-based replicon typing, S1-PFGE and Southern hybridization with ampC and replicon probes. Isolates that could not be characterized were examined for the presence of SXT/R391-like elements. To demonstrate the involvement of these elements in the dissemination of blaCMY-2, we performed a PCR amplification of the integrase (int) and toxin/antitoxin (TA) genes from SXT/R391-like integrative conjugative elements (ICEs). Later on, I-Ceu-I PFGE gels and hybridization with blaCMY-2, int and prfC probes were performed. The genetic organization of blaCMY-2 was also studied. Results ampC genes were located on large conjugative plasmids in 11 of the 19 (58%) P. mirabilis studied. However, in eight of these isolates a plasmid was not involved in the mobilization of ampC genes. I-Ceu-I PFGE and hybridization analyses revealed that blaCMY-2 were chromosomally located in these eight P. mirabilis isolates. The genetic organization of blaCMY-2 and hybridization analyses revealed that blaCMY-2 was carried by an ICE almost identical to ICEPmiJpan1 in seven out of these eight isolates. Conclusions The prevalence of ICEs carrying blaCMY-2 was surprisingly high [37% (7 out of 19)]. This is the first study giving prevalence data on ICEs carrying blaCMY-2 genes. These results suggest the need to study these mobile genetic elements in the context of dissemination of acquired AmpC β-lactamases and also of other β-lactamases, such as extended-spectrum β-lactamases and carbapenemases. [ABSTRACT FROM PUBLISHER]

We report a Serratia marcescens and an Escherichia coli isolate simultaneously detected in the same patient. Both isolates showed susceptibility patterns suggestive of harbouring a plasmid-mediated AmpC β-lactamase (pACBL) and a plasmid-encoded quinolone resistance (PMQR). PCR-based replicon, MOB typing, plasmid profile and Southern hybridization analyses revealed that both isolates coharboured blaDHA-1 and qnrB genes on the same IncL/M-MOBP13 plasmid approximately 70 kb in size. Together with the fact that both plasmids were conjugative in the laboratory, these results strongly suggest that a horizontal transfer event could take place in vivo. This is the first report of an isolate of S. marcescens harbouring a pACBL. The only phenotypic method that suggests the presence of a pACBL in an isolate harbouring an inducible chromosomal AmpC enzyme is the observation of scattered colonies near the edge of the inhibition zones of some β-lactams. The presence of both resistance genes on the same plasmid and the reported increase in PMQR could perhaps explain the widespread distribution of blaDHA-1 genes. [ABSTRACT FROM AUTHOR]

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]

The article discusses a study on the prevalence of carbapenemsase-producing Enterobacteriaceae (CPE) carriers admitted to intensive care units (ICUs) in 11 acute-care Spanish hospitals from 7 different geographical areas. It advises for the implementation of guidelines for the management of the infection control measures to reduce MDR Gram-negative bacteria recommended by ESCMID.

A total of 2440 Escherichia coli strains isolated in 2003 at the Hospital de la Santa Creu i Sant Pau were evaluated for the presence of extended-spectrum β-lactamases. Two different nucleotide sequences that encode the same β-lactamase, CTX-M-14, were detected when the blaCTX-M-14-genes of 35 E. coli isolates were analysed. Thirty-two of the 35 had the previously described sequence of the blaCTX-M-14 ( ), named blaCTX-M-14a, and the remaining three isolates showed a nucleotide sequence identical to that of the blaCTX-M-9 gene except for one nucleotide, named blaCTX-M-14b. Characterisation of the regions surrounding the blaCTX-M-14a showed the IS Ecp1 and the IS 903 upstream and downstream, respectively, of the bla gene, whereas the regions surrounding the blaCTX-M-14b contained the genetic environment described for the blaCTX-M-9 gene, the In 60. Characterisation by hybridisation showed that the blaCTX-M-14a was present in IncK plasmids, whereas the blaCTX-M-14b was found in the HI2 Inc group. The CTX-M-14 ESBL in E. coli isolates is the result of the convergence of two different genes. [ABSTRACT FROM AUTHOR]

Escherichia coli and Salmonella enterica isolates carrying the blaCTX-M-9 gene located on plasmids prevailed at the Hospital de la Santa Creu i Sant Pau, Barcelona, Spain in the 1996–1999 period. The blaCTX-M-9-carrying plasmids showed a great variability in size, suggesting the mobilization of the gene among different plasmid scaffolds. The aim of the present work was to identify and better characterize the plasmids involved in the spread of the blaCTX-M-9 gene. Results showed that the majority of these strains carried plasmids belonging to the IncHI2 incompatibility group. The IncHI2 plasmids were further characterized, and found to be related to the reference IncHI2 plasmid R478. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the incidence of decreased susceptibility to broad-spectrum cephalosporins in Enterobacteriaceae that lack inducible chromosomal bla genes, and to determine the enzymes responsible for resistance. From all clinically relevant Enterobacteriaceae strains isolated between 1994 and 1996, 88 of 7054 Escherichia coli, seven of 581 Klebsiella pneumoniae and 23 of 166 Klebsiella oxytoca strains were studied because of their decreased susceptibilities to broad-spectrum cephalosporins (as reflected in intermediate susceptibilities and/or positive synergy tests and/or irregular crenellated inhibition zones). The most frequent mechanism implicated in decreased susceptibility to broad-spectrum cephalosporins displayed by E. coli and K. oxytoca was hyperproduction of chromosomal beta-lactamase, followed by plasmid-mediated SHV-1 hyperproduction in E. coli. In our hospital, the incidence of plasmid-mediated extended-spectrum beta-lactamases (ESBLs) between 1994 and 1996 was low. ESBLs were found in only 10 (0.14%) E. coli strains (six CTX-M-9, two TEM-12 and two SHV-2), in one (0.17%) K. pneumoniae strain (SHV-2) and in no K. oxytoca strains. The relatively wide variety of beta-lactamases that were detected among these common bacteria isolated from a single medical centre, including non-TEM- and non-SHV-derived ESBLs, appears epidemiologically remarkable. [ABSTRACT FROM AUTHOR]

CMY-2 plasmid-mediated AmpC beta-lactamase (CMY-2) was detected in 21 isolates from two hospitals located in different geographical regions of Spain between October 1999 and December 2000. The isolates comprised two Salmonella enterica serovars (Mikawasima and Montevideo), 16 Escherichia coli, one Klebsiella pneumoniae, one Klebsiella oxytoca and one Proteus mirabilis. In addition to the expected resistance to beta-lactams, including extended-spectrum cephalosporins and cefoxitin, all isolates showed a broad spectrum of associated resistance. All were resistant to sulfamethoxazole, chloramphenicol, tetracycline and streptomycin, and all but two were also resistant to gentamicin. Five isolates were studied in detail and all transferred CMY-2 and other resistance determinants by conjugation. Genomic DNA restriction pattern analysis of the E. coli isolates excluded the dissemination of a single clone. To the best of our knowledge this is the first time that CMY-2 has been detected in P. mirabilis, K. oxytoca and S. enterica serovars Mikawasima and Montevideo. It is also the first time that CMY-2 has been described in Spain. [ABSTRACT FROM AUTHOR]

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.

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.