Product Theaters

Product Theaters provide an opportunity for commercial organizations (Exhibitors) to present information about their product or services or new research findings to the asm2014 attendee in the Product Theater located in the Exhibit Hall. The material presented in Product Theaters may be promotional and may concentrate on a specific product. Therefore, these sessions are considered promotional and do not offer continuing education credits.

 

SUNDAY, MAY 18

Application of Shotgun Metagenomics in Environmental Microbial Ecology

Supported by Illumina, Inc.

11:00 a.m. – 11:45 a.m.
Exhibit Hall
Product Theater Booth #1438

Speakers:
Elisabeth Dinsdale, Ph.D.
Professor, Biology Department, San Diego State University

Program Overview
Next generation sequencing is modernizing the field of microbiology by enabling researchers to look at single microbes in high resolution as well as study changes in microbial communities under changing environmental conditions.  Please join us for a review of recent advances in Illumina’s portfolio of sequencing platforms and applications for microbiology.  We will also hear Dr. Elizabeth Dinsdale discuss the application of shotgun metagenomics in environmental microbial ecology.  Her talk will review how next generation sequencing was used to study whether the microbial community from the water of the kelp forest and the surface of the kelp blade is affected by increased partial pressure of carbon dioxide (pC02), similar to that predicted with global warming.

 

5 Hour Antimicrobial Susceptibility Testing Directly from Positive Blood Cultures

Supported by Accelerate Diagnostics

12:00 p.m. – 12:45 p.m.
Exhibit Hall
Product Theater Booth #1438
Lunch will be provided

Speakers:
Donna M. Wolk, M.H.A., Ph.D., D(ABMM)
System Director, Clinical Microbiology, Geisinger Medical Laboratories

Connie S. Price, M.D.
Chief, Division of Infectious Diseases, Denver Health Medical Center

Program Overview
Antimicrobial susceptibility testing (AST) results are trusted by clinicians to help target effective therapy for patients with serious infections.  However, conventional ID/AST methods take 36-48 hours to produce actionable results, forcing clinicians to prescribe empiric therapy that is often inappropriate or unnecessarily broad-spectrum.  

The goal of the presentation is to introduce a revolutionary sample-to-answer platform that provides 1 hour ID and 5 hour AST direct from samples such as positive blood cultures, respiratory specimens and skin and wound swabs.  The speakers will describe the use of fully-automated microscopy to provide fast, quantitative identification and minimum inhibitory concentration (MIC) results.   In addition, new research data on the performance of the platform with positive blood cultures will be presented.  

 

The Rapid Detection of ampC Resistance Genes in Gram-Negative Bacteria

Supported by Streck

1:00 p.m. – 1:45 p.m.
Exhibit Hall
Product Theater Booth #1438

Speaker:
Dr. Nancy D. Hanson, Ph.D.
Professor and Director of the Center for Research, Anti-Infectives and Biotechnology, Department of Medical Microbiology and Immunology at Creighton University

Program Overview
Infections caused by organisms producing plasmid-mediated AmpC β-lactamases are associated with therapeutic failure. Plasmid-mediated ampC genes are most often found in isolates of Escherichia coli, Klebsiella spp., and Salmonella spp. Identification of the resistance mechanisms responsible for the susceptibility pattern of a clinical isolate can help guide therapy and can be important for surveillance and hospital infection control practices. No CLSI guidelines are in place for the detection of plasmid-mediated AmpC β-lactamases. The gold standard for AmpC detection is an end-point multiplex PCR assay previously designed by our laboratory (Perez JCM 2002). In this presentation a new methodology using rapid amplification PCR technology will be introduced for the amplification of plasmid-mediated ampC genes within 15 minutes. Improvements to the original assay include 1) synthesis and combination of controls from 6 individual control vials to 2 control vials, 2) the addition of an internal control to monitor DNA extraction and amplification, and 3) the use of a primer master mix which combines all the primers in one tube decreasing the individual primer additions from 14 to 1 for each sample. These improvements decrease set-up time and potential pipetting errors with the use of consolidated controls and a primer master mix.

 

MONDAY, MAY 19

Rapid and Reliable Gene Construction with gBlocks® Gene Fragments and Gibson Assembly Method

Supported by Integrated DNA Technologies

11:00 a.m. – 11:45 a.m.
Exhibit Hall
Product Theater Booth #1438
Lunch will be provided

Speaker:
Michel Cannieux, Ph.D., M.B.A.,
Integrated DNA Technologies, Product Commercialization

Program Overview
Gene cloning using PCR is a well-established and effective technique when constructing genes using native DNA sequences. However, when modifying or assembling novel genes, traditional PCR methods can be very inefficient. This often leads researchers to either assemble the new sequence de novo using oligonucleotides or they turn to a gene synthesis service provider to generate such constructs. Integrated DNA Technologies (IDT) now offers in addition to a standard gene synthesis service: a novel, rapid, and reliable method to build and clone the genes you need at a fraction of the cost of full gene synthesis services, using gBlocks. gBlocks® Gene Fragments are double-stranded, sequence-verified DNA blocks up to 2kb base pairs. Their high sequence fidelity and rapid delivery time make gBlocks Gene Fragments ideal for a range of biology applications, including easy assembly of multiple gene fragments to reliably generate larger gene constructs. The goal of this workshop is to enable the bench scientist to use gBlocks to easily and rapidly construct novel DNA sequences using the Gibson Assembly Method.  Products, cloning protocols, and applications will be discussed in addition to troubleshooting recommendations.

 

TUESDAY, MAY 20

Addressing Challenges in Microbiome DNA Analysis

Supported by New England Biolabs, Inc.

11:00 a.m. – 11:45 a.m.
Exhibit Hall
Product Theater Booth #1438

Speaker by topic:

Selective Depletion of Contaminating Vertebrate Host DNA from Microbiome Samples
Erbay Yigit, Ph.D.
New England Biolabs, Inc.

Although total microbiome DNA sequencing is substantially more informative than 16S rRNA analysis, for some sample types sequencing remains cost-prohibitive or even technically infeasible due to host DNA contamination that overwhelms the microbiome DNA. To address this challenge, we developed a magnetic bead-based method, based on CpG methylation density, to separate host DNA from microbial DNA, while maintaining microbial diversity and relative abundance. Utility of this method with a variety of challenging samples will be discussed.

Metagenomics of the Cystic Fibrosis Lung
Yan Wei Lim
Rohwer Lab, San Diego State University

Cystic Fibrosis (CF) is a genetic disorder that leads to dense and un-movable mucus in the airways. In the lung, a complex polymicrobial community becomes established, causing chronic infections, recurrent inflammatory episodes, extensive tissue damage, and shortened life-span. Here, for the first time, we characterize the microbial communities in tissue sections from anatomically distinct regions of ex-planted CF lung samples using a metagenomic approach. Contaminating host DNA was dramatically reduced to ~ 50% of the total sequences, yielding high quality non-human DNA for microbiome analysis. Our results indicate that although the CF lung with advanced disease is mostly colonized by typical CF pathogens, their genetics and spatial distribution are extremely heterogeneous, potentially indicating local disease progression. These findings are distinct from the higher microbial diversity and richness found in patients earlier in disease progression.

 

Microbial Identification Using 16S rRNA Sequence from the Ion Torrent PGM

Supported by Life Technologies

12:00 p.m. – 12:45 p.m.
Exhibit Hall
Product Theater Booth #1438
Lunch will be provided

Speaker:
George S. Watts, Ph.D.
Genomics Shared Service, Co-Director, Arizona Cancer Center, Tucson, AZ

Program Overview
16s rRNA sequence can be useful for identification of microbes in applications from clinical infection to environmental sampling. However, the appropriate choice of hypervariable region(s), analysis methods and interpretation vary by the application. Experience and results using the Ion Torrent PGM with home-brewed and kit approaches to library preparation and sequencing will be discussed along with benchmark data for clinical applications.

 

Specialized Bioinformatics Solutions for Next Generation Sequencing

Supported by ChunLab, Inc.

1:00 p.m. – 1:45 p.m.
Exhibit Hall
Product Theater Booth #1438

Speaker:
Dr. Jongsik Chun
CEO, ChunLab, Inc., Professor, School of Biological Sciences, Seoul National University

Program Overview
Next generation sequencing (NGS) has revolutionized the field of microbiology, with new technologies deciphering DNA sequences faster than ever. However, researchers are now faced with an ever growing challenge of how to make sense of this explosion of data, which is posing major computational challenges. Using carefully chosen, tested and optimized algorithms and biostatistical techniques, ChunLab has developed a series of user friendly software tools that allow researchers to easily browse, analyze and discover their NGS data. Please join us for an overview of ChunLab’s bioinformatics tools and learn how the research community is leveraging them to simplify and accelerate their research. The subject areas that will be covered include: RNA-seq (transcriptomics), microbiome (bacterial and fungal communities) and comparative genomics.

 

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