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Find video protocols related to scientific articles indexed in Pubmed.
Effective method for the heat inactivation of Blastomyces dermatitidis.
Med. Mycol.
PUBLISHED: 07-21-2014
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Manipulation of Blastomyces dermatitidis requires the use of containment level 3 (CL3) practices. However, access to CL3 laboratories is limited and working conditions are restrictive. We describe the validation of a "heat-killing" method to inactivate B. dermatitidis, thus allowing cellular material to be removed from the CL3 laboratory for subsequent DNA isolation that is suitable for genetic applications.
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Is It Time to Centralize High-Risk Cancer Care in the United States? Comparison of Outcomes of Esophagectomy Between England and the United States.
Ann. Surg.
PUBLISHED: 07-01-2014
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To determine the difference in in-hospital mortality and length of hospital stay (LOS) after esophagectomy between the United States and England.
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Previous antibiotic exposure and antimicrobial resistance in invasive pneumococcal disease: results from prospective surveillance.
Clin. Infect. Dis.
PUBLISHED: 06-27-2014
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Estimating the risk of antibiotic resistance is important in selecting empiric antibiotics. We asked how the timing, number of courses, and duration of antibiotic therapy in the previous 3 months affected antibiotic resistance in isolates causing invasive pneumococcal disease (IPD).
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Clinical cure rates in subjects treated with azithromycin for community-acquired respiratory tract infections caused by azithromycin-susceptible or azithromycin-resistant Streptococcus pneumoniae: analysis of Phase 3 clinical trial data.
J. Antimicrob. Chemother.
PUBLISHED: 06-11-2014
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Community-acquired respiratory tract infections (CARTI) are commonly caused by Streptococcus pneumoniae (SPN) and empirically treated with azithromycin. This study assessed clinical cure rates in azithromycin-treated subjects with CARTI caused by azithromycin-susceptible (Azi-S) or azithromycin-resistant (Azi-R) SPN.
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Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 04-14-2014
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We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD(+)-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide.
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The survival of influenza A(H1N1)pdm09 virus on 4 household surfaces.
Am J Infect Control
PUBLISHED: 04-01-2014
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We investigated the survival of a pandemic strain of influenza A H1N1 on a variety of common household surfaces where multiple samples were taken from 4 types of common household fomite at 7 time points. Results showed that influenza A H1N1sw virus particles remained infectious for 48 hours on a wooden surface, for 24 hours on stainless steel and plastic surfaces, and for 8 hours on a cloth surface, although virus recovery from the cloth may have been suboptimal. Our results suggest that pandemic influenza A H1N1 can survive on common household fomites for extended periods of time, and that good hand hygiene and regular disinfection of commonly touched surfaces should be practiced during the influenza season to help reduce transmission.
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Evolution of standardized clinical pathways: refining multidisciplinary care and process to improve outcomes of the surgical treatment of esophageal cancer.
J. Gastrointest. Surg.
PUBLISHED: 03-31-2014
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The aim of this study is to determine the effect of the implementation and evolution of a multidisciplinary esophagectomy care pathway on postoperative outcomes over a 20-year experience.
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In Vitro Activity of New Cephalosporins vs Streptococcus pneumoniae from the Canadian Bacterial Surveillance Network: 2008-2011.
Curr. Microbiol.
PUBLISHED: 02-27-2014
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Between 2008 and 2011, 6,895 Streptococcus pneumoniae isolates were submitted to the Canadian Bacterial Surveillance Network and underwent in vitro susceptibility testing. Fifteen percent of S. pneumoniae isolates were collected from pediatric patients (0-15 years old), 48.6 % of isolates were collected from adults between 16 and 64 years of age, and 36.1 % from adults aged ?65 years; age data were not available for 11 patients. Forty-five percent of S. pneumoniae isolates were recovered from sterile specimens, and 55 % of isolates were from nonsterile specimens. Overall, 0.4 % of isolates were resistant to penicillin, 0.4 % to ceftriaxone, 3 % to amoxicillin, 25 % to erythromycin, and 13 % to trimethoprim/sulfamethoxazole; 6.6 % of isolates were multidrug resistant (MDR). Among MDR isolates, resistance rates exceeded 95 % for erythromycin, tetracycline, and trimethoprim/sulfamethoxazole. The MIC90 of cethromycin, ceftaroline, and ceftobiprole against MDR isolates were 0.12, 0.25, and 1 mg/L, respectively. Ceftaroline, the active form of the prodrug ceftaroline fosamil, exhibited potent in vitro activity against the tested S. pneumoniae including all 456 multidrug-resistant strains. No ceftaroline-resistant isolates were identified.
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Lung resection outcomes and costs in Washington State: a case for regional quality improvement.
Ann. Thorac. Surg.
PUBLISHED: 02-24-2014
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A regional quality improvement effort does not exist for thoracic surgery in the United States. To initiate the development of one, we sought to describe temporal trends and hospital-level variability in associated outcomes and costs of pulmonary resection in Washington (WA) State.
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Characterization of invasive group B streptococcus strains from the greater Toronto area, Canada.
J. Clin. Microbiol.
PUBLISHED: 02-19-2014
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We determined the capsular polysaccharide (CPS) type of 600 group B Streptococcus (GBS) (also known as Streptococcus agalactiae) strains recovered from patients with invasive infections in the greater Toronto area, Canada, between 2009 and 2012. GBS strains of CPS type III were the most prevalent among infants (44% in those with early-onset disease, 75% in those with late-onset disease), while type V strains were most frequently isolated from adult patients (26% in patients?19 years old). We next investigated the presence in our collection of GBS strains belonging to the hypervirulent multilocus sequence typing clonal complex 17 (CC17). We used a PCR test described as specific for the detection of CC17 strains, which targets the gene encoding the major virulence factor HvgA. We identified 91 hvgA-positive strains; of these, 88 were CPS type III, 2 were CPS type IV, and 1 was CPS type V. Using whole-genome sequencing, we showed that the two hvgA-positive CPS type IV strains are CC17 strains which underwent capsular switching. However, sequence analysis revealed that the hvgA-positive CPS type V strain does not belong to CC17 but instead is a bona fide CC1 strain which acquired hvgA, probably by recombination from a CC17 donor. Our findings underline the importance of recombination in GBS pathogenesis and caution against the use of single-gene-based PCR tests to detect CC17 GBS strains.
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Vancomycin-variable Enterococcus faecium: in vivo emergence of vancomycin resistance in a vancomycin-susceptible isolate.
J. Clin. Microbiol.
PUBLISHED: 02-12-2014
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We report the emergence of vancomycin resistance in a patient colonized with a vanA-containing, vanRS-negative isolate of Enterococcus faecium which was initially vancomycin susceptible. This is a previously undescribed mechanism of drug resistance with diagnostic and therapeutic implications.
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Outbreak of vancomycin-susceptible Enterococcus faecium containing the wild-type vanA gene.
J. Clin. Microbiol.
PUBLISHED: 02-12-2014
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Accurate detection of vancomycin-resistant enterococci (VRE) is essential in preventing transmission in health care settings. Chromogenic media are widely used for screening VRE because of fast turnaround times (TAT) and high sensitivity. We report an outbreak of Enterococcus faecium bearing vanA yet susceptible to vancomycin (vancomycin-variable Enterococcus [VVE]). Between October 2009 to March 2011, clinical and screening specimens (n=14,747) were screened for VRE using VRE-selective medium and/or PCR. VVE isolates were genotyped to determine relatedness. Plasmids from these isolates were characterized by sequencing. Overall, 52 VVE isolates were identified, comprising 15% of all VRE isolates identified. Isolates demonstrated growth on Brilliance VRE agar (Oxoid) at 24 h of incubation but did not grow on brain heart infusion agar with 6 ?g/ml vancomycin (Oxoid) or bile esculin azide agar with 6 ?g/ml vancomycin (Oxoid) and were susceptible to vancomycin. Genotyping of 20 randomly selected VVE isolates revealed that 15/20 were identical, while 5 were highly related. PCR of the VVE transposon confirmed the presence of vanHAXY gene cluster; however, vanS (sensor) and vanR (regulator) genes were absent. The outbreak was controlled through routine infection control measures. We report an emergence of a fit strain of E. faecium containing vanA yet susceptible to vancomycin. Whether this new strain represents VRE has yet to be determined; however, unique testing procedures are required for reliable identification of VVE.
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Genomic analysis of Pseudomonas aeruginosa PA96, the host of carbapenem resistance plasmid pOZ176.
FEMS Microbiol. Lett.
PUBLISHED: 02-03-2014
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Pseudomonas aeruginosa PA96 is a clinical isolate from Guangzhou, China, that is multiresistant to antibiotics. We previously described the 500-kb IncP-2 plasmid, pOZ176 that encodes many resistance genes including the IMP-9 carbapenemase. Whole-genome sequencing of PA96 enabled characterization of its genomic islands, virulence factors, and chromosomal resistance genes. We filled gaps using PCR and used optical mapping to confirm the correct contig order. We automatically annotated the core genome and manually annotated the genomic islands. The genome is 6 444 091 bp and encodes 5853 ORFs. From the whole-genome sequence, we constructed a physical map and constructed a phylogenetic tree for comparison with sequenced P. aeruginosa strains. Analysis of known core genome virulence factors and resistance genes revealed few differences with other strains, but the major virulence island is closer to that of DK2 than to PA14. PA96 most closely resembles the environmental strain M18, and notably shares a common serotype, pyoverdin type, flagellar operon, type IV pilin, and several genomic islands with M18.
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The Legionella pneumophila collagen-like protein mediates sedimentation, auto-aggregation and pathogen-phagocyte interactions.
Appl. Environ. Microbiol.
PUBLISHED: 12-13-2013
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Although only partially understood, multi-cellular behavior is relatively common in bacterial pathogens. Bacterial aggregates can resist various host defences and colonize their environment more efficiently than planktonic cells. For the water borne pathogen Legionella pneumophila, little is known about the roles of auto-aggregation or the parameters which allow cell-cell interactions to occur. Here, we determined the endogenous and exogenous factors sufficient to allow auto-aggregation to take place in L. pneumophila. We show that isolates from Legionella species which do not produce the Legionella collagen like protein (Lcl) are deficient in auto-aggregation. Targeted deletion of the Lcl encoding gene (lpg2644) and the addition of Lcl ligands impairs the auto-aggregation of L. pneumophila. In addition, Lcl induced auto-aggregation requires divalent cations. Escherichia coli producing surface exposed Lcl is able to auto-aggregate and shows increased biofilm production. We also demonstrate that L. pneumophila infection of Acanthamoeba castellanii and Hartmanella vermiformis is potentiated under conditions which promote Lcl dependent auto-aggregation. Overall this study shows that L. pneumophila is capable of auto-aggregating in a process that is mediated by Lcl in a divalent cation dependent manner. It also reveals that Lcl potentiates the ability of L. pneumophila to come in contact, attach and infect amoebae.
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Update on clinical impact, documentation, and management of complications associated with esophagectomy.
Thorac Surg Clin
PUBLISHED: 11-09-2013
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The assessment and monitoring of complications associated with esophageal resection suffers from the absence of an internationally recognized system for documenting the incidence and severity of complications. The impact of complications is significant, with direct effects being identified on mortality, length of stay, postoperative quality of life, and long-term survival. Newer systems of assessing surgical complication severity and the resources required to treat complications include the Accordion and Clavien grading systems. New endoscopic and interventional approaches to treating anastomotic leak and stricture and chyle leak can selectively decrease length of stay and costs of managing complications.
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Genetic characterization of seasonal influenza A (H3N2) viruses in Ontario during 2010-2011 influenza season: high prevalence of mutations at antigenic sites.
Influenza Other Respir Viruses
PUBLISHED: 10-26-2013
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The direct effect of antigenic site mutations in influenza viruses on antigenic drift and vaccine effectiveness is poorly understood.
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Streptococcus pneumoniae infection: a Canadian perspective.
Expert Rev Anti Infect Ther
PUBLISHED: 08-28-2013
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Streptococcus pneumoniae infections have resulted in significant morbidity and mortality worldwide in children and adults. In Canada, Streptococcus pneumoniae remains one of the leading causes of infectious disease including pneumonia, meningitis, bacteremia and otitis media. Although the widespread use of pneumococcal conjugate vaccines (PCVs) in Canadian children has reduced the incidence of pneumococcal diseases associated with vaccine-serotypes, rapid increase of non-vaccine serotypes in carriage and pneumococcal infections is of great concern to clinicians. The main goal of this review is to provide an overall picture of invasive pneumococcal diseases (IPD) in Canada for the past few decades, including serotype changes and shifts in antibiotic resistance patterns. The effects of PCV vaccines on incidence, serotype distribution, antibiotic resistance of pneumococcal infections and nasopharyngeal (NP) carriage are discussed. We also examined historical outbreaks of Streptococcus pneumoniae and their public health impact. Recent developments in universal protein vaccines against pneumococcus show promise.
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Macrolide-resistant Mycoplasma pneumoniae in humans, Ontario, Canada, 2010-2011.
Emerging Infect. Dis.
PUBLISHED: 08-24-2013
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Antimicrobial drug resistance rates for Mycoplasma pneumoniae was determined in clinical specimens and isolates obtained during 2011-2012 in Ontario, Canada. Of 91 M. pneumoniae drug-resistant specimens, 11 (12.1%) carried nucleotide mutations associated with macrolide resistance in the 23S rRNA gene. None of the M. pneumoniae specimens were resistant to fluoroquinolones or tetracyclines.
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Biofilms: the stronghold of Legionella pneumophila.
Int J Mol Sci
PUBLISHED: 08-09-2013
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Legionellosis is mostly caused by Legionella pneumophila and is defined as a severe respiratory illness with a case fatality rate ranging from 5% to 80%. L. pneumophila is ubiquitous in natural and anthropogenic water systems. L. pneumophila is transmitted by inhalation of contaminated aerosols produced by a variety of devices. While L. pneumophila replicates within environmental protozoa, colonization and persistence in its natural environment are also mediated by biofilm formation and colonization within multispecies microbial communities. There is now evidence that some legionellosis outbreaks are correlated with the presence of biofilms. Thus, preventing biofilm formation appears as one of the strategies to reduce water system contamination. However, we lack information about the chemical and biophysical conditions, as well as the molecular mechanisms that allow the production of biofilms by L. pneumophila. Here, we discuss the molecular basis of biofilm formation by L. pneumophila and the roles of other microbial species in L. pneumophila biofilm colonization. In addition, we discuss the protective roles of biofilms against current L. pneumophila sanitation strategies along with the initial data available on the regulation of L. pneumophila biofilm formation.
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Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis.
Genome Biol Evol
PUBLISHED: 08-02-2013
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The study of genetic and phenotypic variation is fundamental for understanding the dynamics of bacterial genome evolution and untangling the evolution and epidemiology of bacterial pathogens. Neisseria meningitidis (Nm) is among the most intriguing bacterial pathogens in genomic studies due to its dynamic population structure and complex forms of pathogenicity. Extensive genomic variation within identical clonal complexes (CCs) in Nm has been recently reported and suggested to be the result of homologous recombination, but the extent to which recombination contributes to genomic variation within identical CCs has remained unclear. In this study, we sequenced two Nm strains of identical serogroup (C) and multi-locus sequence type (ST60), and conducted a systematic analysis with an additional 34 Nm genomes. Our results revealed that all gene content variation between the two ST60 genomes was introduced by homologous recombination at the conserved flanking genes, and 94.25% or more of sequence divergence was caused by homologous recombination. Recombination was found in genes associated with virulence factors, antigenic outer membrane proteins, and vaccine targets, suggesting an important role of homologous recombination in rapidly altering the pathogenicity and antigenicity of Nm. Recombination was also evident in genes of the restriction and modification systems, which may undermine barriers to DNA exchange. In conclusion, homologous recombination can drive both gene content variation and sequence divergence in Nm. These findings shed new light on the understanding of the rapid pathoadaptive evolution of Nm and other recombinogenic bacterial pathogens.
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Pneumococcal vaccination programs and the burden of invasive pneumococcal disease in Ontario, Canada, 1995-2011.
Vaccine
PUBLISHED: 07-14-2013
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In 1995, a publicly funded pneumococcal vaccination program for 23-valent polysaccharide vaccine (PPV23) was introduced in Ontario. Conjugate vaccines were authorized in 2001 (PCV7), 2009 (PCV10) and 2010 (PCV13).
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Assessment of Short-Term Clinical Outcomes following Salvage Esophagectomy for the Treatment of Esophageal Malignancy: Systematic Review and Pooled Analysis.
Ann. Surg. Oncol.
PUBLISHED: 07-11-2013
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Combined chemoradiotherapy is increasingly being used as definitive treatment for locoregional esophageal malignancy. Patients with residual or recurrent localized cancer are often selectively considered for salvage esophagectomy (SALV). The aim of this pooled analysis was to compare short-term clinical outcomes from SALV following definitive chemoradiotherapy with those from planned esophagectomy following neoadjuvant chemoradiotherapy (NCRS).
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Toxic shock syndrome: major advances in pathogenesis, but not treatment.
Crit Care Clin
PUBLISHED: 07-09-2013
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Toxic shock syndrome (TSS) is primarily the result of a superantigen-mediated cytokine storm and M protein-mediated neutrophil activation, resulting in the release of mediators leading to respiratory failure, vascular leakage, and shock. Mortality for streptococcal TSS still hovers at 50%. There is evidence to support a role for intravenous immunoglobulin (IVIG) in the treatment of streptococcal TSS. An observational study suggests that an initial conservative surgical approach combined with the use of immune modulators, such as IVIG, may reduce the morbidity associated with extensive surgical exploration in hemodynamically unstable patients without increasing mortality.
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Evolution in surgical management of esophageal cancer.
Dig Dis
PUBLISHED: 06-17-2013
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Esophageal resection remains the primary treatment for local regional esophageal cancer, although its role in superficial (T1A) cancers and squamous cell cancer is in evolution. Mortality associated with esophagectomy has historically been high but is improving with the current expectation of in-hospital mortality rates of 2-4% in high-volume centers. Most patients with regional cancers (T2-4 N0-3) are recommended for neoadjuvant therapy, which most commonly involves radiochemotherapy. Some centers have proposed treating with definitive chemoradiation and reserving surgery for patients who have persistent or recurrent disease. Salvage resections are possible but are associated with higher levels of perioperative morbidity and mortality, and treatment decisions should routinely be based on multidisciplinary discussion in the tumor board. Although open surgical resection (both transthoracic and transhiatal operations) remain the most common approach, minimally invasive or hybrid operations are being done in up to 30% of procedures internationally. There are some indications that minimally invasive esophagectomy may decrease the incidence of respiratory complications and decrease length of stay. At this point, oncologic outcomes appear equivalent between open and minimally invasive procedures. Recent reviews from high-volume esophagectomy centers demonstrate that elderly patients can selectively undergo esophagectomy with the expectation of increased complications but similar mortality and survival to younger patients. Multiple studies confirm that quality of life following esophagectomy can be equivalent to the general population when surgery is done in experienced centers. Patients requiring surgical treatment of esophageal cancer should be referred to high-volume centers, especially those with established care pathways or enhanced recovery programs to improve outcomes including morbidity, mortality, survival, and quality of life.
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Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96.
Antimicrob. Agents Chemother.
PUBLISHED: 05-28-2013
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Pseudomonas aeruginosa 96 (PA96) was isolated during a multicenter surveillance study in Guangzhou, China, in 2000. Whole-genome sequencing of this outbreak strain facilitated analysis of its IncP-2 carbapenem-resistant plasmid, pOZ176. The plasmid had a length of 500,839 bp and an average percent G+C content of 57%. Of the 618 predicted open reading frames, 65% encode hypothetical proteins. The pOZ176 backbone is not closely related to any plasmids thus far sequenced, but some similarity to pQBR103 of Pseudomonas fluorescens SBW25 was observed. Two multiresistant class 1 integrons and several insertion sequences were identified. The blaIMP-9-carrying integron contained aacA4 ? bla(IMP-9) ? aacA4, flanked upstream by Tn21 tnpMRA and downstream by a complete tni operon of Tn402 and a mer module, named Tn6016. The second integron carried aacA4 ? catB8a ? bla(OXA-10) and was flanked by Tn1403-like tnpRA and a sul1-type 3 conserved sequence (3-CS), named Tn6217. Other features include three resistance genes similar to those of Tn5, a tellurite resistance operon, and two pil operons. The replication and maintenance systems exhibit similarity to a genomic island of Ralstonia solanacearum GM1000. Codon usage analysis suggests the recent acquisition of bla(IMP-9). The origins of the integrons on pOZ176 indicated separate horizontal gene transfer events driven by antibiotic selection. The novel mosaic structure of pOZ176 suggests that it is derived from environmental bacteria.
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Risk factors for influenza among health care workers during 2009 pandemic, Toronto, Ontario, Canada.
Emerging Infect. Dis.
PUBLISHED: 05-02-2013
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This prospective cohort study, performed during the 2009 influenza A(H1N1) pandemic, was aimed to determine whether adults working in acute care hospitals were at higher risk than other working adults for influenza and to assess risk factors for influenza among health care workers (HCWs). We assessed the risk for influenza among 563 HCWs and 169 non-HCWs using PCR to test nasal swab samples collected during acute respiratory illness; results for 13 (2.2%) HCWs and 7 (4.1%) non-HCWs were positive for influenza. Influenza infection was associated with contact with family members who had acute respiratory illnesses (adjusted odds ratio [AOR]: 6.9, 95% CI 2.2-21.8); performing aerosol-generating medical procedures (AOR 2.0, 95% CI 1.1-3.5); and low self-reported adherence to hand hygiene recommendations (AOR 0.9, 95% CI 0.7-1.0). Contact with persons with acute respiratory illness, rather than workplace, was associated with influenza infection. Adherence to infection control recommendations may prevent influenza among HCWs.
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Trends in antibiotic resistance over time among pathogens from Canadian hospitals: results of the CANWARD study 2007-11.
J. Antimicrob. Chemother.
PUBLISHED: 04-17-2013
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Antimicrobial resistance patterns change over time and longitudinal surveillance studies provide insight into these trends. We sought to describe the important trends in antimicrobial resistance in key pathogens across Canada to provide useful information to clinicians, policy makers and industry, to assist in optimizing antimicrobial therapy, formulary choices and drug development.
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Iron-deficiency anemia is a common presenting issue with giant paraesophageal hernia and resolves following repair.
J. Gastrointest. Surg.
PUBLISHED: 03-07-2013
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A significant percentage of patients with paraesophageal hernia (PEH) will have a co-existing diagnosis of iron-deficiency anemia which will resolve following surgical repair.
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The impact of neoadjuvant chemoradiotherapy on perioperative outcomes, tumor pathology, and survival in clinical stage II and III esophageal cancer.
Ann. Surg. Oncol.
PUBLISHED: 03-03-2013
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The purpose of this study was to evaluate the impact of neoadjuvant chemoradiotherapy (NCR) on perioperative outcomes, tumor pathology, and survival following surgical resection of clinical stage II and III esophageal cancer.
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The clinical and economic costs of delirium after surgical resection for esophageal malignancy.
Ann. Surg.
PUBLISHED: 02-22-2013
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The aim of this study was to identify preoperative risk factors and postoperative consequences that are associated with the occurrence of delirium after esophagectomy for malignancy.
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Phylogenetic analysis reveals a cryptic species Blastomyces gilchristii, sp. nov. within the human pathogenic fungus Blastomyces dermatitidis.
PLoS ONE
PUBLISHED: 02-14-2013
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Analysis of the population genetic structure of microbial species is of fundamental importance to many scientific disciplines because it can identify cryptic species, reveal reproductive mode, and elucidate processes that contribute to pathogen evolution. Here, we examined the population genetic structure and geographic differentiation of the sexual, dimorphic fungus Blastomyces dermatitidis, the causative agent of blastomycosis.
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What is the relevance of antimicrobial resistance on the outcome of community-acquired pneumonia caused by Streptococcus pneumoniae? (should macrolide monotherapy be used for mild pneumonia?).
Infect. Dis. Clin. North Am.
PUBLISHED: 02-13-2013
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Multidrug-resistant pneumococci continue to increase worldwide. Although there are still questions regarding the relevance of ?-lactam resistance, the recommendation for the use of the macrolides as monotherapy for mild community-acquired pneumonia should be revisited in view of high rates of resistance, the association of clinical failures with low-level and high-level resistance, and the lack of clinical data to support their need for empirical therapy for the atypicals.
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Partially versus fully covered self-expanding metal stents for benign and malignant esophageal conditions: a single center experience.
Surg Endosc
PUBLISHED: 01-31-2013
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Fully covered self-expanding metal stents (FCSEMS), unlike partially covered SEMS (PCSEMS), have been used to treat benign as well as malignant conditions. We aimed to evaluate the outcome of PCSEMS and FCSEMS in patients with both benign and malignant esophageal diseases.
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Neisseria gonorrhoeae treatment failure and susceptibility to cefixime in Toronto, Canada.
JAMA
PUBLISHED: 01-10-2013
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Although cephalosporins are the cornerstone of treatment of Neisseria gonorrhoeae infections, cefixime is the only oral antimicrobial option. Increased minimum inhibitory concentrations (MICs) to cefixime have been identified worldwide and have been associated with reports of clinical failure.
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Comparative Genomic Analyses of Streptococcus pseudopneumoniae Provide Insight into Virulence and Commensalism Dynamics.
PLoS ONE
PUBLISHED: 01-01-2013
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Streptococcus pseudopneumoniae (SPPN) is a recently described species of the viridans group streptococci (VGS). Although the pathogenic potential of S. pseudopneumoniae remains uncertain, it is most commonly isolated from patients with underlying medical conditions, such as chronic obstructive pulmonary disease. S. pseudopneumoniae can be distinguished from the closely related species, S. pneumoniae and S. mitis, by phenotypic characteristics, including optochin resistance in the presence of 5% CO2, bile insolubility, and the lack of the pneumococcal capsule. Previously, we reported the draft genome sequence of S. pseudopneumoniae IS7493, a clinical isolate obtained from an immunocompromised patient with documented pneumonia. Here, we use comparative genomics approaches to identify similarities and key differences between S. pseudopneumoniae IS7493, S. pneumoniae and S. mitis. The genome structure of S. pseudopneumoniae IS7493 is most closely related to that of S. pneumoniae R6, but several recombination events are evident. Analysis of gene content reveals numerous unique features that distinguish S. pseudopneumoniae from other streptococci. The presence of loci for competence, iron transport, pneumolysin production and antimicrobial resistance reinforce the phylogenetic position of S. pseudopneumoniae as an intermediate species between S. pneumoniae and S. mitis. Additionally, the presence of several virulence factors and antibiotic resistance mechanisms suggest the potential of this commensal species to become pathogenic or to contribute to increasing antibiotic resistance levels seen among the VGS.
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Comparative Genomics Reveal That Host-Innate Immune Responses Influence the Clinical Prevalence of Legionella pneumophila Serogroups.
PLoS ONE
PUBLISHED: 01-01-2013
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Legionella pneumophila is the primary etiologic agent of legionellosis, a potentially fatal respiratory illness. Amongst the sixteen described L. pneumophila serogroups, a majority of the clinical infections diagnosed using standard methods are serogroup 1 (Sg1). This high clinical prevalence of Sg1 is hypothesized to be linked to environmental specific advantages and/or to increased virulence of strains belonging to Sg1. The genetic determinants for this prevalence remain unknown primarily due to the limited genomic information available for non-Sg1 clinical strains. Through a systematic attempt to culture Legionella from patient respiratory samples, we have previously reported that 34% of all culture confirmed legionellosis cases in Ontario (n?=?351) are caused by non-Sg1 Legionella. Phylogenetic analysis combining multiple-locus variable number tandem repeat analysis and sequence based typing profiles of all non-Sg1 identified that L. pneumophila clinical strains (n?=?73) belonging to the two most prevalent molecular types were Sg6. We conducted whole genome sequencing of two strains representative of these sequence types and one distant neighbour. Comparative genomics of the three L. pneumophila Sg6 genomes reported here with published L. pneumophila serogroup 1 genomes identified genetic differences in the O-antigen biosynthetic cluster. Comparative optical mapping analysis between Sg6 and Sg1 further corroborated this finding. We confirmed an altered O-antigen profile of Sg6, and tested its possible effects on growth and replication in in vitro biological models and experimental murine infections. Our data indicates that while clinical Sg1 might not be better suited than Sg6 in colonizing environmental niches, increased bloodstream dissemination through resistance to the alternative pathway of complement mediated killing in the human host may explain its higher prevalence.
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Group A Streptococcus emm gene types in pharyngeal isolates, Ontario, Canada, 2002-2010.
Emerging Infect. Dis.
PUBLISHED: 11-22-2011
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Group A Streptococcus (GAS) is a human-adapted pathogen that causes a variety of diseases, including pharyngitis and invasive infections. GAS strains are categorized by variation in the nucleotide sequence of the gene (emm) that encodes the M protein. To identify the emm types of GAS strains causing pharyngitis in Ontario, Canada, we sequenced the hypervariable region of the emm gene in 4,635 pharyngeal GAS isolates collected during 2002-2010. The most prevalent emm types varied little from year to year. In contrast, fine-scale geographic analysis identified inter-site variability in the most common emm types. Additionally, we observed fluctuations in yearly frequency of emm3 strains from pharyngitis patients that coincided with peaks of emm3 invasive infections. We also discovered a striking increase in frequency of emm89 strains among isolates from patients with pharyngitis and invasive disease. These findings about the epidemiology of GAS are potentially useful for vaccine research.
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Extensive genomic variation within clonal complexes of Neisseria meningitidis.
Genome Biol Evol
PUBLISHED: 11-14-2011
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Meningococcal disease is a widely distributed complex disease affecting all age categories. It can cause severe meningitis and septicemia, especially in unvaccinated infants and young children. The causative agent, Neisseria meningitidis (Nm), can be phenotypically and genetically differentiated into serogroups and sequence types (STs) and has a highly dynamic population structure. To obtain a deeper understanding of the epidemiology of Nm, we sequenced seven Nm genomes. Large-scale genomic analysis was conducted with these 7 Nm genomes, 27 additional Nm genomes from GenBank, and 4 other Neisseria genomes. We observed extensive homologous recombination in all gene functional categories among different Nm genomes. Homologous recombination is so frequent that it has resulted in numerous chimeric open reading frames, including genes in the capsule biosynthesis cluster and loci targeted by commercial vaccines. Our results reveal that, despite widespread use, evolutionary relationships inferred from the standard seven-gene multilocus sequence typing (MLST) method could not predict virulence gene content or strain phenotype. In fact, up to 28% of the virulence-associated genes could differ between strains of identical STs. Consistent with previous studies, we found that allelic recombination is also associated with alterations in antibiotic susceptibility. Overall, these findings emphasize the extensive genomic plasticity of Nm and the limitations of standard molecular methods to quantify this genotypic and phenotypic diversity.
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Advances in the management of esophageal perforation.
Thorac Surg Clin
PUBLISHED: 11-02-2011
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Therapy for acute esophageal perforation in the last decade has benefited from newer technology in endoscopy and imaging. Success with nonoperative therapies such as endoluminal stenting and clipping has improved outcomes and shortened length of stay in selected patients. Iatrogenic injury currently comprises most acute esophageal perforation, and nonoperative therapy may be appropriate in a significant percentage of patients. The decision regarding operative vs non-operative therapy is best done by a dedicated surgical team with experience in all the surgical and endoscopic treatment options. Boerhaave syndrome occurs less often and may be treated with endoscopic therapy, although it more likely requires operative intervention. This article reviews current advances in the diagnosis and management of acute esophageal perforation.
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The impact of influenza on the Canadian First Nations.
Can J Public Health
PUBLISHED: 10-29-2011
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In March and April 2009, pandemic H1N1 2009 influenza A virus (pH1N1 2009) emerged among residents of and travelers to Mexico, the United States and Canada. During the 2009 pandemic, cases of pH1N1 2009 infection were reported from over 214 countries, with at least 18,449 recorded deaths. In Canada, over 8,500 cases were hospitalized, 16.8% of which required intensive care. A particularly concerning occurrence was the spread of pH1N1 2009 into First Nations communities in Canada. Although Aboriginal peoples constitute only 3.8% of Canadas population, members of the First Nations were 6.5 times more likely to be admitted to an ICU with pH1N1 2009 influenza than non-First Nations, and had rates of hospitalization nearly triple that of the national cumulative crude rate for all Canadians. We herein provide a succinct review of our current understanding of the risk of influenza among First Nations populations in Canada.
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Whole-genome sequence of Streptococcus pseudopneumoniae isolate IS7493.
J. Bacteriol.
PUBLISHED: 10-14-2011
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Streptococcus pseudopneumoniae is a member of the viridans group streptococci (VGS) whose pathogenic significance is unclear. We announce the complete genome sequence of S. pseudopneumoniae IS7493. The genome sequence will assist in the characterization of this new organism and facilitate the development of accurate diagnostic assays to distinguish it from Streptococcus pneumoniae and Streptococcus mitis.
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Volume-outcome relationship in surgery for esophageal malignancy: systematic review and meta-analysis 2000-2011.
J. Gastrointest. Surg.
PUBLISHED: 09-15-2011
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The aim of this study is to provide a contemporary quantitative analysis of the existing literature examining the relationship between surgical caseload and outcome following esophageal resection.
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Non-invasive cytology brush PCR diagnostic testing in mucosal leishmaniasis: superior performance to conventional biopsy with histopathology.
PLoS ONE
PUBLISHED: 08-23-2011
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Traditional methods of diagnosing mucosal leishmaniasis (ML), such as biopsy with histopathology, are insensitive and require collection of an invasive diagnostic specimen.
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Identification of sexual networks through molecular typing of quinolone-resistant Neisseria gonorrhoeae in Ontario, Canada.
Sex Transm Dis
PUBLISHED: 08-17-2011
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Neisseria gonorrhoeae multi-antigen sequence typing technique demonstrated multiple sexual transmission networks in Ontario, Canada. Isolates with novel sequences had higher odds of originating in Toronto but had no association with heightened population-level quinolone exposure. Neisseria gonorrhoeae multi-antigen sequence typing technique can be a useful tool for investigation of multidrug-resistant N. gonorrhoeae emergence in North America.
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Multidrug-resistant pandemic (H1N1) 2009 infection in immunocompetent child.
Emerging Infect. Dis.
PUBLISHED: 08-02-2011
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Recent case reports describe multidrug-resistant influenza A pandemic (H1N1) 2009 virus infection in immunocompromised patients exposed to neuraminidase inhibitors because of an I223R neuraminidase mutation. We report a case of multidrug-resistant pandemic (H1N1) 2009 bearing the I223R mutation in an ambulatory child with no previous exposure to neuraminidase inhibitors.
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Evaluation and verification of the Seeplex Diarrhea-V ACE assay for simultaneous detection of adenovirus, rotavirus, and norovirus genogroups I and II in clinical stool specimens.
J. Clin. Microbiol.
PUBLISHED: 07-20-2011
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Acute viral gastroenteritis is an intestinal infection that can be caused by several different viruses. Here we describe the evaluation and verification of Seeplex Diarrhea-V ACE (Seeplex DV), a novel commercial multiplex reverse transcription-PCR (RT-PCR) assay that detects 5 diarrheal pathogens, including adenovirus, rotavirus, norovirus genogroup I (GI) and GII, and astrovirus. We describe a retrospective study of 200 clinical specimens of which 177 were stool specimens previously tested for the presence of gastrointestinal viruses by electron microscopy (EM) and/or real-time RT-PCR (rRT-PCR). The remaining 23 specimens comprised other human pathogens of viral or bacterial origin. Discordant norovirus GI and GII results were resolved using a commercial kit; discordant adenovirus and rotavirus results were resolved using a home brew multiplex rRT-PCR assay. Diagnostic sensitivities and specificities were calculated before and after discordant analysis. After discordant analysis, estimated diagnostic sensitivities were 100% for adenovirus, rotavirus, and norovirus GI and 97% for norovirus GII. Diagnostic specificities after discordant analysis were 100% for adenovirus, rotavirus, and norovirus GI and 99.4% for norovirus GII. The 95% limits of detection were 31, 10, 2, and 1 genome equivalent per reaction for adenovirus, rotavirus, and norovirus GI and GII, respectively. The results demonstrate that the Seeplex DV assay is sensitive, specific, convenient, and reliable for the simultaneous detection of several viral pathogens directly in specimens from patients with gastroenteritis. Importantly, this novel multiplex PCR assay enabled the identification of viral coinfections in 12 (6.8%) stool specimens.
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Repair of giant paraesophageal hernias routinely produces improvement in respiratory function.
J. Thorac. Cardiovasc. Surg.
PUBLISHED: 06-21-2011
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Assessment of the clinical impact of giant paraesophageal hernias have historically focused on upper gastrointestinal symptoms. This study assesses the effect of paraesophageal hernia repair on respiratory function.
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Susceptibility of Streptococcus pneumoniae to fluoroquinolones in Canada.
Antimicrob. Agents Chemother.
PUBLISHED: 05-31-2011
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Ciprofloxacin, the first fluoroquinolone to be used to treat lower respiratory tract infections (LRTI), demonstrates poor potency against Streptococcus pneumoniae, and its use has been associated with the emergence of resistance. During the last decade, fluoroquinolones with enhanced in vitro activity against S. pneumoniae have replaced ciprofloxacin for the treatment of LRTI. Here, we analyzed the impact of more active fluoroquinolone usage on pneumococci by examining the fluoroquinolone usage, prevalence of fluoroquinolone resistance, and mutations in the genes that encode the major target sites for the fluoroquinolones (gyrA and parC) in pneumococcal isolates collected in Canada-wide surveillance. A total of 26,081 isolates were collected between 1998 and 2009. During this time period, total per capita outpatient use of fluoroquinolones increased from 64 to 96 prescriptions per 1,000 persons per year. The proportion of prescriptions for respiratory tract infection that were for fluoroquinolones increased from 5.9% to 10.7%, but the distribution changed: the proportion of prescriptions for ciprofloxacin decreased from 5.3% to 0.5%, and those for levofloxacin or moxifloxacin increased from 1.5% in 1999 to 5.9% in 2009. The prevalence of ciprofloxacin resistance (MIC ? 4 ?g/ml), levofloxacin resistance, and moxifloxacin resistance remained unchanged at <2%. Multivariable analyses showed that prevalence of mutations known to be associated with reduced susceptibility to fluoroquinolones did not change during the surveillance period. If fluoroquinolone therapy is required, the preferential use of fluoroquinolones with enhanced pneumococcal activity to treat pneumococcal infections may slow the emergence of resistance in S. pneumoniae.
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Update on staging and surgical treatment options for esophageal cancer.
J. Gastrointest. Surg.
PUBLISHED: 04-14-2011
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Esophageal cancer remains a challenging clinical problem, with overall long-term survivorship consistently at a level of approximately 30%. The incidence of esophageal cancer is increasing worldwide, with the most dramatic increase being seen with respect to esophageal adenocarcinoma.
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FOCUS 2: a randomized, double-blinded, multicentre, Phase III trial of the efficacy and safety of ceftaroline fosamil versus ceftriaxone in community-acquired pneumonia.
J. Antimicrob. Chemother.
PUBLISHED: 04-13-2011
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Ceftaroline (active form of the prodrug ceftaroline fosamil) is a novel cephalosporin with activity against pathogens commonly associated with community-acquired pneumonia (CAP), including Streptococcus pneumoniae and Gram-negative pathogens. This randomized, double-blind, Phase III study evaluated the efficacy and safety of ceftaroline fosamil in treating patients with CAP. The primary objective was to determine non-inferiority [lower limit of 95% confidence interval (CI) ? -10%] of clinical cure rates achieved with ceftaroline fosamil compared with those achieved with ceftriaxone in the clinically evaluable (CE) and modified intent-to-treat efficacy (MITTE) populations.
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FOCUS 1: a randomized, double-blinded, multicentre, Phase III trial of the efficacy and safety of ceftaroline fosamil versus ceftriaxone in community-acquired pneumonia.
J. Antimicrob. Chemother.
PUBLISHED: 04-13-2011
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Ceftaroline, the active form of the prodrug ceftaroline fosamil, is a novel cephalosporin with bactericidal activity against important pathogens associated with community-acquired pneumonia (CAP), including Streptococcus pneumoniae and common Gram-negative pathogens. FOCUS 1 is a randomized, double-blinded, Phase III study that was conducted to evaluate the efficacy and safety of ceftaroline fosamil in treating patients with CAP. The primary objective was to determine non-inferiority [lower limit of 95% confidence interval (CI) ? -10%] in clinical cure rates achieved with ceftaroline fosamil compared with those achieved with ceftriaxone in the clinically evaluable (CE) and modified intent-to-treat efficacy (MITTE) populations.
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Respiratory illnesses in Canadian health care workers: a pilot study of influenza vaccine and oseltamivir prophylaxis during the 2007/2008 influenza season.
Influenza Other Respir Viruses
PUBLISHED: 04-05-2011
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Data regarding both rates of acute respiratory illness in health care workers and experience with long-term antiviral prophylaxis are sparse.
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Systemic dysregulation of angiopoietin-1/2 in streptococcal toxic shock syndrome.
Clin. Infect. Dis.
PUBLISHED: 04-05-2011
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Streptococcal toxic shock syndrome (STSS) is characterized by diffuse vascular leak resulting from widespread endothelial activation. Angiopoietin-1 and -2 (Ang-1 and Ang-2), which are important regulators of endothelial quiescence and activation, respectively, are dysregulated in certain diseases that are associated with endothelial dysfunction, but they have not been previously investigated in STSS. Plasma Ang-1 and Ang-2 concentrations were measured in 37 patients with invasive streptococcal infection with and without concurrent STSS. Greater angiopoietin dysregulation (decreased Ang-1 and increased Ang-2) occurred in STSS than in invasive infection without shock; dysregulation decreased with convalescence. These results suggest that systemic Ang-1 and Ang-2 dysregulation is associated with disease severity in invasive streptococcal infection and that plasma levels of Ang-1 and Ang-2 may serve as clinically informative biomarkers in STSS.
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Polymerase chain reaction detection of Leishmania kDNA from the urine of Peruvian patients with cutaneous and mucocutaneous leishmaniasis.
Am. J. Trop. Med. Hyg.
PUBLISHED: 04-05-2011
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We hypothesized that Leishmania kDNA may be present in urine of patients with cutaneous leishmaniasis (CL). Urine samples and standard diagnostic specimens were collected from patients with skin lesions. kDNA polymerase chain reaction (PCR) was performed on samples from patients and 10 healthy volunteers from non-endemic areas. Eighty-six of 108 patients were diagnosed with CL and 18 (21%) had detectable Leishmania Viannia kDNA in the urine. Sensitivity and specificity were 20.9% (95% confidence interval [CI] 12.3-29.5%) and 100%. Six of 8 patients with mucocutaneous involvement had detectable kDNA in urine versus 12 of 78 patients with isolated cutaneous disease (P < 0.001). L. (V.) braziliensis (N = 3), L. (V.) guyanensis (N = 6), and L. (V.) peruviana (N = 3) were identified from urine. No healthy volunteer or patient with an alternate diagnosis had detectable kDNA in urine. Sensitivity of urine PCR is sub-optimal for diagnosis. On the basis of these preliminary data in a small number of patients, detectable kDNA in urine may identify less localized forms of infection and inform treatment decisions.
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Diagnosis and management of anastomotic leaks after esophagectomy.
J. Gastrointest. Surg.
PUBLISHED: 03-24-2011
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Complications following esophagectomy significantly affect outcomes, including perioperative mortality, costs, and survival. Anastomotic leak remains one of the most serious complications, and early recognition and appropriate initial treatment are essential.
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Comparative evaluation of a chromogenic agar medium, the modified Hodge test, and a battery of meropenem-inhibitor discs for detection of carbapenemase activity in Enterobacteriaceae.
J. Clin. Microbiol.
PUBLISHED: 03-23-2011
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Three phenotypic methods (modified Hodge test, chromogenic agar, and meropenem discs combined with specific inhibitors) used for the detection of carbapenemase activity were tested on a panel of characterized Enterobacteriaceae expressing various ?-lactamase mechanisms. Overall, the meropenem-plus-inhibitor approach was more sensitive and specific than the other methods, despite its limitation of being unable to detect class D carbapenemases.
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Lcl of Legionella pneumophila is an immunogenic GAG binding adhesin that promotes interactions with lung epithelial cells and plays a crucial role in biofilm formation.
Infect. Immun.
PUBLISHED: 03-21-2011
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Legionellosis is mostly caused by Legionella pneumophila and is defined by a severe respiratory illness with a case fatality rate ranging from 5 to 80%. In vitro and in vivo, interactions of L. pneumophila with lung epithelial cells are mediated by the sulfated glycosaminoglycans (GAGs) of the host extracellular matrix. In this study, we have identified several Legionella heparin binding proteins. We have shown that one of these proteins, designated Lcl, is a polymorphic adhesin of L. pneumophila that is produced during legionellosis. Homologues of Lcl are ubiquitous in L. pneumophila serogroups but are undetected in other Legionella species. Recombinant Lcl binds to GAGs, and a ?lpg2644 mutant demonstrated reduced binding to GAGs and human lung epithelial cells. Importantly, we showed that the ?lpg2644 strain is dramatically impaired in biofilm formation. These data delineate the role of Lcl in the GAG binding properties of L. pneumophila and provide molecular evidence regarding its role in L. pneumophila adherence and biofilm formation.
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Pertussis resurgence in Toronto, Canada: a population-based study including test-incidence feedback modeling.
BMC Public Health
PUBLISHED: 03-19-2011
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Pertussis continues to challenge medical professionals; recently described increases in incidence may be due to age-cohort effects, vaccine effectiveness, or changes in testing patterns. Toronto, Canada has recently experienced increases in pertussis incidence, and provides an ideal jurisdiction for evaluating pertussis epidemiology due to centralized testing. We evaluated pertussis trends in Toronto using all available specimen data, which allowed us to control for changing testing patterns and practices.
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Modified multiple-locus variable-number tandem-repeat analysis for rapid identification and typing of Clostridium difficile during institutional outbreaks.
J. Clin. Microbiol.
PUBLISHED: 03-16-2011
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A modified multiple-locus variable-number tandem-repeat analysis (MMLVA) method was validated on Clostridium difficile-infected stool specimens from institutional outbreaks. The method allows simultaneous detection of toxin genes, deletions, and tandem repeats from cultured isolates or stool specimens. Results were used to aid institutional outbreak investigation by identifying clusters of NAP1/027.
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Distribution of antiseptic resistance genes qacA, qacB, and smr in methicillin-resistant Staphylococcus aureus isolated in Toronto, Canada, from 2005 to 2009.
Antimicrob. Agents Chemother.
PUBLISHED: 03-14-2011
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Decreased susceptibility to chlorhexidine gluconate (CHDN) in methicillin-resistant Staphylococcus aureus (MRSA) is associated with the qacA, qacB, and smr genes, encoding efflux pumps. A total of 334 MRSA isolates were collected from two Canadian intensive care units between 2005 and 2009. We identified the qacAB genes in 7 strains (2%; 2 qacA genes and 5 qacB genes) and the smr gene in 23 (7%) strains. CHDN minimal bactericidal concentrations were slightly higher for strains harboring smr genes.
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Open versus minimally invasive esophagectomy: what is the best approach? Frame the issue.
J. Gastrointest. Surg.
PUBLISHED: 03-08-2011
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Surgical resection continues to be the gold standard treatment approach for early invasive and locoregional esophageal cancer. Esophagectomy has historically had a reputation as a complex operation with high mortality and morbidity. Increasingly, results from high-volume specialized centers have demonstrated that mortality rates of below 4% should be expected and that patients can potentially demonstrate excellent levels of quality of life following surgical resection. Up until recently, virtually all surgical resections were done utilizing an open approach utilizing either a transthoracic or a transhiatal operation. Over the past several years, however, a variety of fully minimally invasive or hybrid procedures have been advocated with a view of improving mortality and morbidity outcomes. In the absence of either randomized or controlled prospective comparisons, this series of papers will review current perceptions of the advantages of both minimally invasive and open surgery for the treatment of esophageal cancer.
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Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 03-07-2011
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Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is a human-adapted bacterium that causes a range of infections. Much effort has been expended to dissect the molecular basis of invasive (sterile-site) infections, but little is known about the genomes of strains causing pharyngitis (streptococcal "sore throat"). Additionally, there is essentially nothing known about the genetic relationships between populations of invasive and pharyngitis strains. In particular, it is unclear if invasive strains represent a distinct genetic subpopulation of strains that cause pharyngitis. We compared the genomes of 86 serotype M3 GAS pharyngitis strains with those of 215 invasive M3 strains from the same geographical location. The pharyngitis and invasive groups were highly related to each other and had virtually identical phylogenetic structures, indicating they belong to the same genetic pool. Despite the overall high degree of genetic similarity, we discovered that strains from different host environments (i.e., throat, normally sterile sites) have distinct patterns of diversifying selection at the nucleotide level. In particular, the pattern of polymorphisms in the hyaluronic acid capsule synthesis operon was especially different between the two strain populations. This finding was mirrored by data obtained from full-genome analysis of strains sequentially cultured from nonhuman primates. Our results answer the long-standing question of the genetic relationship between GAS pharyngitis and invasive strains. The data provide previously undescribed information about the evolutionary history of pathogenic microbes that cause disease in different anatomical sites.
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Novel mutations in a patient isolate of Streptococcus agalactiae with reduced penicillin susceptibility emerging after long-term oral suppressive therapy.
Antimicrob. Agents Chemother.
PUBLISHED: 03-07-2011
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Penicillin nonsusceptibility has been demonstrated in group B streptococci (GBS), but there is limited information regarding mechanisms of resistance. We report a case of GBS with reduced susceptibility to penicillin emerging after long-term suppressive oral penicillin therapy for a prosthetic joint infection. Molecular characterization of the isolate before and after long-term penicillin therapy revealed 5 mutations in the ligand-binding regions of PBP1a, -2a, and -2x not previously reported in GBS.
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Antimicrobial susceptibility of 15,644 pathogens from Canadian hospitals: results of the CANWARD 2007-2009 study.
Diagn. Microbiol. Infect. Dis.
PUBLISHED: 03-01-2011
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The CANWARD study (Canadian Ward Surveillance Study) assessed the antimicrobial susceptibility of a variety of available agents against 15 644 pathogens isolated from patients in Canadian hospitals between 2007 and 2009. The most active (based on MIC data) agents against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci were daptomycin, linezolid, tigecycline, and vancomycin (MRSA only) with MIC(90)s (?g/mL) of 0.25 and 2, 2 and 2, 0.5 and 0.12, and 1, respectively. The most active agents against extended-spectrum ?-lactamase-producing Escherichia coli were colistin (polymyxin E), doripenem, ertapenem, meropenem, and tigecycline with MIC(90)s (?g/mL) of 1, ? 0.12, 0.25, ? 0.12, and 1, respectively. The most active agents against Pseudomonas aeruginosa were amikacin, cefepime, ceftazidime, colistin, doripenem, meropenem, and piperacillin-tazobactam with MIC(90)s (?g/mL) of 32, 16, 32, 2, 4, 8, and 64, respectively. Overall, the most active agents versus Gram-positive cocci from Canadian hospitals were vancomycin, linezolid, daptomycin, and tigecycline and versus Gram-negative bacilli were amikacin, cefepime, doripenem, ertapenem (excluding Pseudomonas aeruginosa), meropenem, piperacillin-tazobactam, and tigecycline (excluding Pseudomonas aeruginosa).
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Analytical and clinical validation of novel real-time reverse transcriptase-polymerase chain reaction assays for the clinical detection of swine-origin H1N1 influenza viruses.
Diagn. Microbiol. Infect. Dis.
PUBLISHED: 01-22-2011
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During the early stages of the 2009/2010 swine-origin H1N1 influenza A (S-OIV H1N1 FluA) outbreak, the development and validation of sensitive and specific detection methods were a priority for rapid and accurate diagnosis. Between May and June 2009, 2 real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) assays targeting the hemagglutinin and neuraminidase genes of the S-OIV H1N1 FluA virus were developed. These assays are highly specific, showing no cross-reactivity against a panel of respiratory viruses and can differentiate S-OIV H1N1 from seasonal FluA viruses. Analytical sensitivities of the 2 assays were found to be 10(-1) tissue culture infectious dose, 50%/ml. Clinical testing showed 99.2% sensitivity and 94.6-98.1% specificity. A large prospective analysis showed that 94.8-95.5% of S-OIV positive specimens were negative by seasonal H1/H3 subtyping. The large-scale validation data presented in this report indicate that these novel assays provide an accurate and efficient method for the rapid detection of S-OIV H1N1 FluA viruses.
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Neuraminidase-inhibitor resistance testing for pandemic influenza A (H1N1) 2009 in Ontario, Canada.
J. Clin. Virol.
PUBLISHED: 01-19-2011
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Oseltamivir resistance-associated H275Y mutation in the neuraminidase (NA) gene of pandemic influenza A (H1N1) 2009 was occasionally reported worldwide during the 2009-2010 influenza season. A significant proportion of those were found in immunocompromised or severely ill persons. This phenomenon remains infrequent and clear recommendations for resistance testing are lacking.
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Evolving management strategies in esophageal perforation: surgeons using nonoperative techniques to improve outcomes.
J. Am. Coll. Surg.
PUBLISHED: 01-15-2011
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Management of acute esophageal perforation continues to evolve. We hypothesized that treatment of these patients at a tertiary referral center is more important than beginning treatment within 24 hours, and that the evolving application of nonsurgical treatment techniques by surgeons would produce improved outcomes.
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Development of a molecular-beacon-based multi-allelic real-time RT-PCR assay for the detection of human coronavirus causing severe acute respiratory syndrome (SARS-CoV): a general methodology for detecting rapidly mutating viruses.
Arch. Virol.
PUBLISHED: 01-11-2011
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Emerging infectious diseases have caused a global effort for development of fast and accurate detection techniques. The rapidly mutating nature of viruses presents a major difficulty, highlighting the need for specific detection of genetically diverse strains. One such infectious agent is SARS-associated coronavirus (SARS-CoV), which emerged in 2003. This study aimed to develop a real-time RT-PCR detection assay specific for SARS-CoV, taking into account its intrinsic polymorphic nature due to genetic drift and recombination and the possibility of continuous and multiple introductions of genetically non-identical strains into the human population, by using mismatch-tolerant molecular beacons designed to specifically detect the SARS-CoV S, E, M and N genes. These were applied in simple, reproducible duplex and multiplex real-time PCR assays on 25 post-mortem samples and constructed RNA controls, and they demonstrated high target detection ability and specificity. This assay can readily be adapted for detection of other emerging and rapidly mutating pathogens.
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Diagnostic performance of filter paper lesion impression PCR for secondarily infected ulcers and nonulcerative lesions caused by cutaneous leishmaniasis.
J. Clin. Microbiol.
PUBLISHED: 12-22-2010
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We compared traditional cutaneous leishmaniasis diagnostic methods to filter paper lesion impression (FPLI) PCR for secondarily infected ulcers and nonulcerative lesions. The sensitivity and specificity of FPLI PCR for secondarily infected lesions (n = 8) were 100%. In primarily nonulcerative lesions (n = 15), the sensitivity of FPLI PCR was inferior to that of pooled-invasive-specimen PCR (72.7% versus 100%) (P = 0.10). FPLI PCR is sensitive, specific, and unlike invasive procedures, can be used in secondarily infected ulcers. Invasive specimen collection is superior in nonulcerative lesions.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.