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1.  Rectal ulcer: Due to ketoprofen, argon plasma coagulation and prostatic brachytherapy 
World Journal of Gastroenterology : WJG  2014;20(45):17244-17246.
Prostatic brachytherapy with permanent seed implants is a recent and safe radiation therapy technique associated with radiation-induced digestive disease. Argon plasma coagulation procedure is a validated modality in the management of haemorrhagic radiation proctitis, which is known to occasionally induce chronic rectal ulcers. We report here an original case report of an acute painful rectal ulcer as a consequence of the combination of short-term therapy with non-steroidal anti-inflammatory drugs therapy, prostatic brachytherapy with malposition of seed implants and argon plasma coagulation procedure in a patient with haemorrhagic radiation proctitis. The description of this clinical observation is essential to recommend the discontinuation of non-steroidal anti-inflammatory drugs therapy and the control of the position of seed implants in case of prostatic brachytherapy before argon plasma coagulation for radiation-induced proctitis.
doi:10.3748/wjg.v20.i45.17244
PMCID: PMC4258597  PMID: 25493041
Radiation proctitis; Prostatic brachytherapy; Argon plasma coagulation; Non-steroidal anti-inflammatory drugs
2.  Carriage of extended-spectrum beta-lactamase-producing enterobacteriacae among internal medicine patients in Switzerland 
Background
The incidence of extended-spectrum beta-lactamase producing-enterobacteriacae (ESBL-E) infection is rising worldwide. We aimed to determine the prevalence and nosocomial acquisition rate of ESBL-E as well as the risk factors for ESBL-E carriage and acquisition amongst patients consecutively admitted to 13 internal medicine units at our hospital who were not previously known to be ESBL-E carriers.
Findings
We screened all patients admitted or transferred to internal medicine units for ESBL-E on admission and discharge using rectal swabs. Of 1072 patients screened, 51 (4.8%) were carriers of an ESBL-E at admission. Of 473 patients who underwent admission and discharge screening, 21 (4.4%) acquired an ESBL-E. On multivariate analysis, diabetes mellitus without end-organ complications (OR 2.87 [1.09-7.08]), connective tissue disease (OR 7.22 [1.17-44.59]), and liver failure (OR 8.39 [1.55-45.45]) were independent risk factors for carriage of an ESBL-E upon admission to hospital (area under the ROC curve, 0.68). Receipt of a first- or second-generation cephalosporin (OR 9.25 [2.22-37.82]), intra-hospital transfer (OR 6.68 [1.71-26.06]), and a hospital stay >21 days (OR 25.17 [4.18-151.68]) were associated with acquisition of an ESBL-E during hospitalisation; whilst admission from home was protective (OR 0.16 [0.06-0.39]) on univariate regression. No risk profile with sufficient accuracy to predict previously unknown carriage on admission or acquisition of ESBL-E could be developed using readily available patient information.
Conclusions
ESBL-E carriage is endemic amongst internal medicine patients at our institution. We were unable to develop a clinical risk profile to accurately predict ESBL-E carriage amongst these patients.
doi:10.1186/2047-2994-2-20
PMCID: PMC3711782  PMID: 23759067
Extended-spectrum beta-lactamase producing enterobacteraciae; Infection control; Antimicrobial resistance
3.  Methicillin-resistant Staphylococcus aureus risk profiling: who are we missing? 
Background
Targeted screening of patients at high risk for methicillin-resistant Staphylococcus aureus (MRSA) carriage is an important component of MRSA control programs, which rely on prediction tools to identify those high-risk patients. Most previous risk studies reported a substantial rate of patients who are eligible for screening, but failed to be enrolled. The characteristics of these missed patients are seldom described. We aimed to determine the rate and characteristics of patients who were missed by a MRSA screening programme at our institution to see how the failure to include these patients might impact the accuracy of clinical prediction tools.
Findings
From March-June 2010 all patients admitted to 13 internal medicine wards at the University of Geneva Hospital (HUG) were prospectively screened for MRSA carriage. Of 1968 patients admitted to the ward, 267 patients (13.6%) failed to undergo appropriate MRSA screening. Forty-one (2.4%) screened patients were MRSA carriers at admission. On multivariate regression, patients who were missed by screening were more likely to be aged < 50 years (OR 2.4 [1.4-3.9]), transferred to internal medicine from another ward in the hospital (OR 2.8 [1.1-7.1]), and have a history of malignancy (OR 3.2[2.1-5.1]). There was no significant difference in the rate of previous MRSA carriage between screened and unscreened patients.
Conclusions
Our findings highlight the potential bias that “missed” patients may introduce into MRSA risk scores. Reporting on the proportions and characteristics of missed patients is essential for accurate interpretation of MRSA prediction tools.
doi:10.1186/2047-2994-2-17
PMCID: PMC3672049  PMID: 23721630
Carrier state; Epidemiology; MRSA; Prevalence; Probability; Predictive value of tests; Staphylococcal infection; Switzerland
4.  Endoscopic ultrasonography-guided fine needle aspiration: Relatively low sensitivity in the endosonographer population 
AIM: To assess the characteristics and quality of endoscopic ultrasonography-guided fine needle aspiration (EUS-FNA) in a large panel of endosonographers.
METHODS: A survey was conducted during the 13th annual live course of endoscopic ultrasonography (EUS) held in Amsterdam, Netherlands. A 2-page questionnaire was developed for the study. Content validity of the questionnaire was determined based on input by experts in the field and a review of the relevant literature. It contained 30 questions that pertained to demographics and the current practice for EUS-FNA of responders, including sampling technique, sample processing, cytopathological diagnosis and sensitivity of EUS-FNA for the diagnosis of solid mass lesions. One hundred and sixty-one endosonographers who attended the course were asked to answer the survey. This allowed assessing the current practice of EUS-FNA as well as the self-reported sensitivity of EUS-FNA for the diagnosis of solid mass lesions. We also examined which factors were associated with a self-reported sensitivity of EUS-FNA for the diagnosis of solid mass lesions > 80%.
RESULTS: Completed surveys were collected from 92 (57.1%) of 161 endosonographers who attended the conference. The endosonographers had been practicing endoscopy and EUS for 12.5 ± 7.8 years and 4.8 ± 4.1 years, respectively; one third of them worked in a hospital with an annual caseload > 100 EUS-FNA. Endoscopy practices were located in 29 countries, including 13 countries in Western Europe that totaled 75.3% of the responses. Only one third of endosonographers reported a sensitivity for the diagnosis of solid mass lesions > 80% (interquartile range of sensitivities, 25.0%-75.0%). Factors independently associated with a sensitivity > 80% were (1) > 7 needle passes for pancreatic lesions or rapid on-site cytopathological evaluation (ROSE) (P < 0.0001), (2) a high annual hospital caseload (P = 0.024) and (3) routine isolation of microcores from EUS-FNA samples (P = 0.042). ROSE was routinely available to 27.9% of respondents. For lymph nodes and pancreatic masses, a maximum of three needle passes was performed by approximately two thirds of those who did not have ROSE. Microcores were routinely harvested from EUS-FNA samples by approximately one third (37.2%) of survey respondents.
CONCLUSION: EUS-FNA sensitivity was considerably lower than reported in the literature. Low EUS-FNA sensitivity was associated with unavailability of ROSE, few needle passes, absence of microcore isolation and low hospital caseload.
doi:10.3748/wjg.v18.i19.2357
PMCID: PMC3353369  PMID: 22654426
Caseload; Community surveys; Cytopathology; Endoscopic ultrasonography; Histopathology; Quality improvement
5.  Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21 
Nature genetics  2008;40(5):631-637.
In a genome-wide association study to identify loci associated with colorectal cancer (CRC) risk, we genotyped 555,510 SNPs in 1,012 early-onset Scottish CRC cases and 1,012 controls (phase 1.) In phase 2, we genotyped the 15,008 highest-ranked SNPs in 2,057 Scottish cases and 2,111 controls. We then genotyped the five highest-ranked SNPs from the joint phase 1 and 2 analysis in 14,500 cases and 13,294 controls from seven populations, and identified a previously unreported association, rs3802842 on 11q23 (OR = 1.1; P = 5.8 × 10-10), showing population differences in risk. We also replicated and fine-mapped associations at 8q24 (rs7014346; OR = 1.19; P = 8.6 × 10-26) and 18q21 (rs4939827; OR = 1.2; P = 7.8 × 10-28). Risk was greater for rectal than for colon cancer for rs3802842 (P < 0.008) and rs4939827 (P < 0.009). Carrying all six possible risk alleles yielded OR = 2.6 (95% CI = 1.75-3.89) for CRC. These findings extend our understanding of the role of common genetic variation in CRC etiology.
doi:10.1038/ng.133
PMCID: PMC2778004  PMID: 18372901
6.  Multiple Loci With Different Cancer Specificities Within the 8q24 Gene Desert 
Recent studies based on genome-wide association, linkage, and admixture scan analysis have reported associations of various genetic variants in 8q24 with susceptibility to breast, prostate, and colorectal cancer. This locus lies within a 1.18-Mb region that contains no known genes but is bounded at its centromeric end by FAM84B and at its telomeric end by c-MYC, two candidate cancer susceptibility genes. To investigate the associations of specific loci within 8q24 with specific cancers, we genotyped the nine previously reported cancer-associated single-nucleotide polymorphisms across the region in four case–control sets of prostate (1854 case subjects and 1894 control subjects), breast (2270 case subjects and 2280 control subjects), colorectal (2299 case subjects and 2284 control subjects), and ovarian (1975 case subjects and 3411 control subjects) cancer. Five different haplotype blocks within this gene desert were specifically associated with risks of different cancers. One block was solely associated with risk of breast cancer, three others were associated solely with the risk of prostate cancer, and a fifth was associated with the risk of prostate, colorectal, and ovarian cancer, but not breast cancer. We conclude that there are at least five separate functional variants in this region.
doi:10.1093/jnci/djn190
PMCID: PMC2902819  PMID: 18577746
7.  Association Study of Prostate Cancer Susceptibility Variants with Risks of Invasive Ovarian, Breast, and Colorectal Cancer 
Cancer research  2008;68(21):8837-8842.
Several prostate cancer susceptibility loci have recently been identified by genome-wide association studies. These loci are candidates for susceptibility to other epithelial cancers. The aim of this study was to test these tag single nucleotide polymorphisms (SNP) for association with invasive ovarian, colorectal, and breast cancer. Twelve prostate cancer-associated tag SNPs were genotyped in ovarian (2,087 cases/3,491 controls), colorectal (2,148 cases/2,265 controls) and breast (first set, 4,339 cases/4,552controls; second set, 3,800 cases/3,995 controls) case-control studies. The primary test of association was a comparison of genotype frequencies between cases and controls, and a test for trend stratified by study where appropriate. Genotype-specific odds ratios (OR) were estimated by logistic regression. SNP rs2660753 (chromosome 3p12) showed evidence of association with ovarian cancer [per minor allele OR, 1.19; 95% confidence interval (95% CI), 1.04-1.37; Ptrend = 0.012]. This association was stronger for the serous histologic subtype (OR, 1.29; 95% CI, 1.09-1.53; P = 0.003). SNP rs7931342 (chromosome 11q13) showed some evidence of association with breast cancer (per minor allele OR, 0.95; 95% CI, 0.91-0.99; Ptrend = 0.028). This association was somewhat stronger for estrogen receptor-positive tumors (OR, 0.92; 95% CI, 0.87-0.98; P = 0.011). None of these tag SNPs were associated with risk of colorectal cancer. In conclusion, loci associated with risk of prostate cancer may also be associated with ovarian and breast cancer susceptibility. However, the effects are modest and warrant replication in larger studies.
doi:10.1158/0008-5472.CAN-08-2363
PMCID: PMC2666188  PMID: 18974127
8.  Somatically acquired hypomethylation of IGF2 in breast and colorectal cancer 
Human Molecular Genetics  2008;17(17):2633-2643.
The imprinted insulin-like growth factor 2 (IGF2) gene is expressed predominantly from the paternal allele. Loss of imprinting (LOI) associated with hypomethylation at the promoter proximal sequence (DMR0) of the IGF2 gene was proposed as a predisposing constitutive risk biomarker for colorectal cancer. We used pyrosequencing to assess whether IGF2 DMR0 methylation is either present constitutively prior to cancer or whether it is acquired tissue-specifically after the onset of cancer. DNA samples from tumour tissues and matched non-tumour tissues from 22 breast and 42 colorectal cancer patients as well as peripheral blood samples obtained from colorectal cancer patients [SEARCH (n=case 192, controls 96)], breast cancer patients [ABC (n=case 364, controls 96)] and the European Prospective Investigation of Cancer [EPIC-Norfolk (n=breast 228, colorectal 225, controls 895)] were analysed. The EPIC samples were collected 2–5 years prior to diagnosis of breast or colorectal cancer. IGF2 DMR0 methylation levels in tumours were lower than matched non-tumour tissue. Hypomethylation of DMR0 was detected in breast (33%) and colorectal (80%) tumour tissues with a higher frequency than LOI indicating that methylation levels are a better indicator of cancer than LOI. In the EPIC population, the prevalence of IGF2 DMR0 hypomethylation was 9.5% and this correlated with increased age not cancer risk. Thus, IGF2 DMR0 hypomethylation occurs as an acquired tissue-specific somatic event rather than a constitutive innate epimutation. These results indicate that IGF2 DMR0 hypomethylation has diagnostic potential for colon cancer rather than value as a surrogate biomarker for constitutive LOI.
doi:10.1093/hmg/ddn163
PMCID: PMC2515372  PMID: 18541649
9.  Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers 
BMC Genomics  2006;7:296.
Background
To unravel molecular targets involved in glycopeptide resistance, three isogenic strains of Staphylococcus aureus with different susceptibility levels to vancomycin or teicoplanin were subjected to whole-genome microarray-based transcription and quantitative proteomic profiling. Quantitative proteomics performed on membrane extracts showed exquisite inter-experimental reproducibility permitting the identification and relative quantification of >30% of the predicted S. aureus proteome.
Results
In the absence of antibiotic selection pressure, comparison of stable resistant and susceptible strains revealed 94 differentially expressed genes and 178 proteins. As expected, only partial correlation was obtained between transcriptomic and proteomic results during stationary-phase. Application of massively parallel methods identified one third of the complete proteome, a majority of which was only predicted based on genome sequencing, but never identified to date. Several over-expressed genes represent previously reported targets, while series of genes and proteins possibly involved in the glycopeptide resistance mechanism were discovered here, including regulators, global regulator attenuator, hyper-mutability factor or hypothetical proteins. Gene expression of these markers was confirmed in a collection of genetically unrelated strains showing altered susceptibility to glycopeptides.
Conclusion
Our proteome and transcriptome analyses have been performed during stationary-phase of growth on isogenic strains showing susceptibility or intermediate level of resistance against glycopeptides. Altered susceptibility had emerged spontaneously after infection with a sensitive parental strain, thus not selected in vitro. This combined analysis allows the identification of hundreds of proteins considered, so far as hypothetical protein. In addition, this study provides not only a global picture of transcription and expression adaptations during a complex antibiotic resistance mechanism but also unravels potential drug targets or markers that are constitutively expressed by resistant strains regardless of their genetic background, amenable to be used as diagnostic targets.
doi:10.1186/1471-2164-7-296
PMCID: PMC1687195  PMID: 17121677
10.  Rapid Staphylococcus aureus agr Type Determination by a Novel Multiplex Real-Time Quantitative PCR Assay 
Journal of Clinical Microbiology  2006;44(5):1892-1895.
The accessory gene regulator (agr) is a crucial regulatory component of Staphylococcus aureus involved in the control of bacterial virulence factor expression. We developed a real-time multiplex quantitative PCR assay for the rapid determination of S. aureus agr type. This assay represents a rapid and affordable alternative to sequence-based strategies for assessing relevant epidemiological information.
doi:10.1128/JCM.44.5.1892-1895.2006
PMCID: PMC1479209  PMID: 16672433
11.  Use of Oligoarrays for Characterization of Community-Onset Methicillin-Resistant Staphylococcus aureus 
Journal of Clinical Microbiology  2006;44(3):1040-1048.
Until recently, methicillin-resistant Staphylococcus aureus (MRSA) was considered the prototype of a hospital-acquired bacterial pathogen. However, recent reports have shown that MRSA has now emerged in the community. Characterization of specific markers for distinguishing the origin of isolates could contribute to improved knowledge of MRSA epidemiology. The release of whole-genome sequences of hospital- and community-acquired S. aureus strains allowed the development of whole-genome content analysis techniques, including microarrays. We developed a microarray composed of 8,191 open reading frame-specific oligonucleotides covering >99% of the four sequenced S. aureus genomes (N315, Mu50, MW2, and COL) to evaluate gene contents of hospital- and community-onset S. aureus strains. In parallel, pulsed-field gel electrophoresis, variable number of tandem repeats, antibiogram, staphylococcal cassette chromosome-mec element typing, and presence of the Panton-Valentine leukocidin gene were evaluated in a collection of 15 clinical isolates. Clusters obtained with microarrays showed a high degree of similarity with those obtained by pulsed-field gel electrophoresis or variable number of tandem repeats. Clusters clearly segregated hospital-onset strains from community-onset strains. Moreover, the microarray approach allowed definition of novel marker genes and chromosomal regions specific for given groups of isolates, thus providing better discrimination and additional information compared to pulsed-field gel electrophoresis and variable number of tandem repeats. Finally, the comparative genome hybridization approach unraveled the occurrence of multiple horizontal transfer events leading to community-onset MRSA as well as the need for a specific genetic background in recipient strains for both the acquisition and the stability of the mec element.
doi:10.1128/JCM.44.3.1040-1048.2006
PMCID: PMC1393086  PMID: 16517892
12.  Community-associated Methicillin-resistant Staphylococcus aureus, Switzerland 
Emerging Infectious Diseases  2005;11(6):962-965.
Two case-control studies evaluated the prevalence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) carriage at hospital admission and characteristics of patients with CA-MRSA. Among 14,253 patients, CA-MRSA prevalence was 0.9/1,000 admissions. Although 5 CA-MRSA isolates contained Panton-Valentine leukocidin, only 1 patient had a previous skin infection. No easily modifiable risk factor for CA-MRSA was identified.
doi:10.3201/eid1106.041308
PMCID: PMC3367580  PMID: 15963298
Keywords: Staphylococcus aureus; methicillin resistance; prevalence; Switzerland; community; risk factor

Results 1-12 (12)