This document outlines a proposed experimental design to study the development of microbial communities in a hospital setting. It involves daily sampling from patient rooms, staff, and surfaces over the course of a year to determine how human demographics and environmental factors shape the microbiome. Key hypotheses focus on how microbial succession is driven by occupancy and influenced by existing communities. Quantitative analysis of samples using DNA sequencing aims to identify sources and patterns of contamination over time.
The study aims to determine how human demographics and environmental factors shape the development of microbial communities in hospitals. Samples will be collected daily from patient rooms, staff, surfaces and air/water sources for a year from a newly opened hospital. The data will help understand how microbial succession occurs and how prior occupants influence colonization by pathogens. Quantitative PCR and sequencing will identify microbes, with analyses predicting community changes from environmental shifts.
Molecular biomarkers can be used for several purposes in infectious disease research and clinical practice. These include detecting pathogens, measuring antibody responses, identifying markers of virulence, resistance, and disease severity, and understanding human immune responses and genetic susceptibility. Challenges include lack of sensitivity, mobile genetic elements, and changes in RNA sequences. Whole genome sequencing allows investigation of microbial phylogeny, evolution, and virulence factors.
This presents a number of case studies on the application on high-throughput sequencing (HTS), next generation sequencing (NGS), to biological problems ranging from human genome sequencing, identification of disease mutations, metagenomics, virus discovery, epidemic, transmission chains and viral populations. Presented at the University of Glasgow on Friday 26th June 2015.
This presentation discusses novel technologies to study the resistome, which is the collection of antibiotic resistance genes found in an environment. It describes culture-based and culture-independent methods to analyze the resistome, including metagenomic shotgun sequencing, functional metagenomics, and high-throughput quantitative PCR. The presentation also details a study that used these methods to analyze the gut resistome of ICU patients receiving intensive antibiotic therapy and found a rich diversity of resistance genes that increased during their hospital stay. Long-read nanopore sequencing is also presented as an upcoming method to map resistomes by linking resistance genes to mobile genetic elements.
This document discusses a presentation on microbiome identification and characterization technologies. It begins with an introduction to the human microbiome and catalogs our "second genome". It then discusses how technologies like 16S rRNA sequencing and metagenomics have unlocked the ability to study the microbiome. Population studies of microbiome composition and disease associations are also reviewed. The presentation goes on to provide examples of how to design assays to identify and profile relevant microbiome targets, and discusses solutions for identification and profiling in microbiome research.
Clinical Metagenomics for Rapid Detection of Enteric Pathogens and Characteri...QIAGEN
High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.
Dr. Ben Hause - Pathogen Discovery Using Metagenomic SequencingJohn Blue
Pathogen Discovery Using Metagenomic Sequencing - Dr. Ben Hause, College of Veterinary Medicine, Kansas State University, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
The study aims to determine how human demographics and environmental factors shape the development of microbial communities in hospitals. Samples will be collected daily from patient rooms, staff, surfaces and air/water sources for a year from a newly opened hospital. The data will help understand how microbial succession occurs and how prior occupants influence colonization by pathogens. Quantitative PCR and sequencing will identify microbes, with analyses predicting community changes from environmental shifts.
Molecular biomarkers can be used for several purposes in infectious disease research and clinical practice. These include detecting pathogens, measuring antibody responses, identifying markers of virulence, resistance, and disease severity, and understanding human immune responses and genetic susceptibility. Challenges include lack of sensitivity, mobile genetic elements, and changes in RNA sequences. Whole genome sequencing allows investigation of microbial phylogeny, evolution, and virulence factors.
This presents a number of case studies on the application on high-throughput sequencing (HTS), next generation sequencing (NGS), to biological problems ranging from human genome sequencing, identification of disease mutations, metagenomics, virus discovery, epidemic, transmission chains and viral populations. Presented at the University of Glasgow on Friday 26th June 2015.
This presentation discusses novel technologies to study the resistome, which is the collection of antibiotic resistance genes found in an environment. It describes culture-based and culture-independent methods to analyze the resistome, including metagenomic shotgun sequencing, functional metagenomics, and high-throughput quantitative PCR. The presentation also details a study that used these methods to analyze the gut resistome of ICU patients receiving intensive antibiotic therapy and found a rich diversity of resistance genes that increased during their hospital stay. Long-read nanopore sequencing is also presented as an upcoming method to map resistomes by linking resistance genes to mobile genetic elements.
This document discusses a presentation on microbiome identification and characterization technologies. It begins with an introduction to the human microbiome and catalogs our "second genome". It then discusses how technologies like 16S rRNA sequencing and metagenomics have unlocked the ability to study the microbiome. Population studies of microbiome composition and disease associations are also reviewed. The presentation goes on to provide examples of how to design assays to identify and profile relevant microbiome targets, and discusses solutions for identification and profiling in microbiome research.
Clinical Metagenomics for Rapid Detection of Enteric Pathogens and Characteri...QIAGEN
High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.
Dr. Ben Hause - Pathogen Discovery Using Metagenomic SequencingJohn Blue
Pathogen Discovery Using Metagenomic Sequencing - Dr. Ben Hause, College of Veterinary Medicine, Kansas State University, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
Microbiome Identification to Characterization: Pathogen Detection Webinar Ser...QIAGEN
This document discusses the development of rapid detection methods for microbial and microbiome analysis and their applications to human health. It provides an overview of QIAGEN's microbial qPCR products and discusses focused metagenomics applications like screening for antibiotic resistance genes in the food supply and human gut. Limitations of current methods are outlined and the benefits of qPCR for rapid, specific, and sensitive microbial detection are described.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
The Global Virome Project is a 10-year global effort to identify and characterize naturally occurring viruses with pandemic potential. It aims to build a comprehensive database of the estimated 1.6 million viral species circulating in mammals and waterfowl. This will allow researchers to develop broad-spectrum countermeasures against future zoonotic viruses and identify high-risk viruses to prevent spillover. The project will sample viruses in 108 sites across 63 countries over 10 years, prioritizing countries and species based on viral discovery rates and zoonotic risk prediction models. The goal is to capture over 85% of the global mammalian virome to transform virology and pandemic preparedness.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
This document discusses the application of whole genome sequencing in infectious disease diagnostics. It provides examples of how genome sequencing has been used to identify bacterial species, detect antibiotic resistance genes, and study outbreaks. The document also discusses challenges around regulatory approval of genomic tests, data sharing policies, and database management. Overall, it argues that whole genome sequencing is a valuable tool but that standards must be developed to ensure high quality data.
The document discusses the rise of big data in microbiology due to decreasing costs of DNA sequencing and computational resources. It describes how high-throughput sequencing is generating vast amounts of microbial genomic and metagenomic data. However, analyzing these large, complex datasets presents numerous technical and social challenges for microbiologists, including handling data volume, integrating diverse data types, accessing resources, and incentivizing data sharing. Overcoming these bottlenecks will be key to unlocking the scientific insights contained within the microbial "big data" tidal wave.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.3- Next Generation Sequencing. Technologies and Applications. Part III: NGS Applications II.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Profiling Hospital-Acquired Pathogens and Antibiotic Resistance Genes WebinarQIAGEN
Hospital-acquired infections (HAIs) are caused by bacterial, viral and fungal pathogens that easily spread through the body. The most common HAIs include urinary tract infections, bloodstream infections and pneumonia. HAIs are becoming more virulent and more resistant to the antibiotics typically used to fight them, making antibiotic resistance a serious public health concern. In this webinar, we will provide an overview of hospital-acquired pathogens and antibiotic resistance. We will also present tools to help you identify and characterize hospital-acquired bacterial species and antibiotic resistance genes in your research samples.
Building bioinformatics resources for the global communityExternalEvents
1. The document evaluates different methods for inferring relationships between Salmonella samples based on whole genome sequencing data from large databases. It compares k-mer based methods and site-based methods using 18,997 Salmonella isolates from public databases.
2. Site-based methods like NUCmer and MLST produced more accurate results, but require more computing resources when dealing with large databases. K-mer based methods are faster but more sensitive to assembly and contamination issues.
3. While k-mer methods may be useful for initial filtering, site-based methods are superior for accuracy, though challenges remain in applying them to databases containing tens of thousands of samples. Quality control and computing resources are important considerations.
Global surveillance One World – One HealthExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Global surveillance One World – One Health. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
This document describes a study that uses next-generation re-sequencing and bioinformatics to analyze presence/absence variation of accessory chromosomes across isolates of the wheat pathogen Zymoseptoria tritici. The genome of the reference isolate IPO323 contains 21 chromosomes including 8 accessory chromosomes. Low-cost next-generation sequencing of 13 novel Z. tritici isolates is performed and the reads are aligned to the IPO323 reference genome to determine if accessory chromosomes present in IPO323 are also present in the novel isolates based on read coverage. De novo assembly of reads from the novel isolates is also conducted and compared to IPO323 to identify any additional accessory chromosomes or sequences not present in IPO323. This
Web applications for rapid microbial taxonomy identification ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Web applications for rapid microbial taxonomy identification. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Metagenomics is the study of genetic material recovered directly from environmental samples. It provides a new approach to studying microbes that are not easily cultured in a laboratory and enables investigation of microbial communities in their natural habitats. Metagenomics involves directly extracting DNA from samples, sequencing it, and analyzing the genetic information obtained from entire communities of organisms simultaneously. This provides insights into uncultured microbes and their roles in various environments.
This document discusses the potentials and pitfalls of metagenomics. It begins with an introduction to metagenomics and its history. It describes some of the early applications of metagenomics including exploration of microbial communities and identification of specific functions. Potential pitfalls of metagenomics are then outlined, including issues related to DNA extraction, sequencing depth, and biases. The major pitfall discussed is the incompleteness of databases for assigning taxonomy and functions. The document concludes by describing some of the potentials of metagenomics, including hunting for novel antibiotic resistance genes using functional metagenomics and extracting genomes from metagenomes through reducing microdiversity and binning sequences from multiple related samples.
This document presents information on quorum sensing in archaea. It defines quorum sensing as a mechanism by which microbes regulate gene expression in response to population density through the production and detection of signaling molecules called autoinducers. The document discusses the history of quorum sensing, mechanisms, types of signaling, and examples of quorum sensing in certain archaeal species such as Natronococcus occultus and Methanosaeta harundinacea. It also outlines potential applications and future research directions regarding quorum sensing in archaea.
Xenotransplantation involves transplanting organs or tissues from other animal species into humans as a way to address the shortage of human organs available for transplant. While research in this area is progressing, there are still concerns about immune rejection and the potential transmission of animal diseases to humans. Several biotech and pharmaceutical companies have active xenotransplantation programs focused on developing methods to prevent rejection and testing the use of pig organs in clinical trials. Regulatory agencies in the US and UK are providing oversight and guidance on clinical research in this emerging field.
I ,sree, from INDIA , am a Operations Head for 'Lalitha Foundation' which is a charitable trust for tribal and rural people in Andhra Pradesh, India.
Our Mission: The mission of the 'Lalitha Foundation' is to access to Modern technology for people with lack of health services in rural and tribal areas.
Priority areas addressed: Consultations with Expert Doctors through video - conference, Training for Primary Health Care.
The document proposes constructing a one-storey residential building to address the client's housing needs. It will include three bedrooms, two kitchens, and a porch. The building will cost approximately 1.15 million pesos to build and will solve the client's current problems of high rental costs and transportation expenses, while providing a comfortable living environment. Facility requirements like appliances, electricity, and water access are also addressed. The construction is proposed to alleviate the client's housing issues for many years.
Microbiome Identification to Characterization: Pathogen Detection Webinar Ser...QIAGEN
This document discusses the development of rapid detection methods for microbial and microbiome analysis and their applications to human health. It provides an overview of QIAGEN's microbial qPCR products and discusses focused metagenomics applications like screening for antibiotic resistance genes in the food supply and human gut. Limitations of current methods are outlined and the benefits of qPCR for rapid, specific, and sensitive microbial detection are described.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
The Global Virome Project is a 10-year global effort to identify and characterize naturally occurring viruses with pandemic potential. It aims to build a comprehensive database of the estimated 1.6 million viral species circulating in mammals and waterfowl. This will allow researchers to develop broad-spectrum countermeasures against future zoonotic viruses and identify high-risk viruses to prevent spillover. The project will sample viruses in 108 sites across 63 countries over 10 years, prioritizing countries and species based on viral discovery rates and zoonotic risk prediction models. The goal is to capture over 85% of the global mammalian virome to transform virology and pandemic preparedness.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
This document discusses the application of whole genome sequencing in infectious disease diagnostics. It provides examples of how genome sequencing has been used to identify bacterial species, detect antibiotic resistance genes, and study outbreaks. The document also discusses challenges around regulatory approval of genomic tests, data sharing policies, and database management. Overall, it argues that whole genome sequencing is a valuable tool but that standards must be developed to ensure high quality data.
The document discusses the rise of big data in microbiology due to decreasing costs of DNA sequencing and computational resources. It describes how high-throughput sequencing is generating vast amounts of microbial genomic and metagenomic data. However, analyzing these large, complex datasets presents numerous technical and social challenges for microbiologists, including handling data volume, integrating diverse data types, accessing resources, and incentivizing data sharing. Overcoming these bottlenecks will be key to unlocking the scientific insights contained within the microbial "big data" tidal wave.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.3- Next Generation Sequencing. Technologies and Applications. Part III: NGS Applications II.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Profiling Hospital-Acquired Pathogens and Antibiotic Resistance Genes WebinarQIAGEN
Hospital-acquired infections (HAIs) are caused by bacterial, viral and fungal pathogens that easily spread through the body. The most common HAIs include urinary tract infections, bloodstream infections and pneumonia. HAIs are becoming more virulent and more resistant to the antibiotics typically used to fight them, making antibiotic resistance a serious public health concern. In this webinar, we will provide an overview of hospital-acquired pathogens and antibiotic resistance. We will also present tools to help you identify and characterize hospital-acquired bacterial species and antibiotic resistance genes in your research samples.
Building bioinformatics resources for the global communityExternalEvents
1. The document evaluates different methods for inferring relationships between Salmonella samples based on whole genome sequencing data from large databases. It compares k-mer based methods and site-based methods using 18,997 Salmonella isolates from public databases.
2. Site-based methods like NUCmer and MLST produced more accurate results, but require more computing resources when dealing with large databases. K-mer based methods are faster but more sensitive to assembly and contamination issues.
3. While k-mer methods may be useful for initial filtering, site-based methods are superior for accuracy, though challenges remain in applying them to databases containing tens of thousands of samples. Quality control and computing resources are important considerations.
Global surveillance One World – One HealthExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Global surveillance One World – One Health. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
This document describes a study that uses next-generation re-sequencing and bioinformatics to analyze presence/absence variation of accessory chromosomes across isolates of the wheat pathogen Zymoseptoria tritici. The genome of the reference isolate IPO323 contains 21 chromosomes including 8 accessory chromosomes. Low-cost next-generation sequencing of 13 novel Z. tritici isolates is performed and the reads are aligned to the IPO323 reference genome to determine if accessory chromosomes present in IPO323 are also present in the novel isolates based on read coverage. De novo assembly of reads from the novel isolates is also conducted and compared to IPO323 to identify any additional accessory chromosomes or sequences not present in IPO323. This
Web applications for rapid microbial taxonomy identification ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Web applications for rapid microbial taxonomy identification. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Metagenomics is the study of genetic material recovered directly from environmental samples. It provides a new approach to studying microbes that are not easily cultured in a laboratory and enables investigation of microbial communities in their natural habitats. Metagenomics involves directly extracting DNA from samples, sequencing it, and analyzing the genetic information obtained from entire communities of organisms simultaneously. This provides insights into uncultured microbes and their roles in various environments.
This document discusses the potentials and pitfalls of metagenomics. It begins with an introduction to metagenomics and its history. It describes some of the early applications of metagenomics including exploration of microbial communities and identification of specific functions. Potential pitfalls of metagenomics are then outlined, including issues related to DNA extraction, sequencing depth, and biases. The major pitfall discussed is the incompleteness of databases for assigning taxonomy and functions. The document concludes by describing some of the potentials of metagenomics, including hunting for novel antibiotic resistance genes using functional metagenomics and extracting genomes from metagenomes through reducing microdiversity and binning sequences from multiple related samples.
This document presents information on quorum sensing in archaea. It defines quorum sensing as a mechanism by which microbes regulate gene expression in response to population density through the production and detection of signaling molecules called autoinducers. The document discusses the history of quorum sensing, mechanisms, types of signaling, and examples of quorum sensing in certain archaeal species such as Natronococcus occultus and Methanosaeta harundinacea. It also outlines potential applications and future research directions regarding quorum sensing in archaea.
Xenotransplantation involves transplanting organs or tissues from other animal species into humans as a way to address the shortage of human organs available for transplant. While research in this area is progressing, there are still concerns about immune rejection and the potential transmission of animal diseases to humans. Several biotech and pharmaceutical companies have active xenotransplantation programs focused on developing methods to prevent rejection and testing the use of pig organs in clinical trials. Regulatory agencies in the US and UK are providing oversight and guidance on clinical research in this emerging field.
I ,sree, from INDIA , am a Operations Head for 'Lalitha Foundation' which is a charitable trust for tribal and rural people in Andhra Pradesh, India.
Our Mission: The mission of the 'Lalitha Foundation' is to access to Modern technology for people with lack of health services in rural and tribal areas.
Priority areas addressed: Consultations with Expert Doctors through video - conference, Training for Primary Health Care.
The document proposes constructing a one-storey residential building to address the client's housing needs. It will include three bedrooms, two kitchens, and a porch. The building will cost approximately 1.15 million pesos to build and will solve the client's current problems of high rental costs and transportation expenses, while providing a comfortable living environment. Facility requirements like appliances, electricity, and water access are also addressed. The construction is proposed to alleviate the client's housing issues for many years.
The document outlines the process for planning a new hospital, including forming a planning team, conducting feasibility studies, and implementing the project. Key steps involve assessing community health needs, selecting an appropriate site, developing construction plans, procuring equipment and staff, and commissioning the new facility once built. The planning process aims to establish adequate healthcare services through strategic planning and consideration of factors like infrastructure, resources, and community demographics.
1. The document discusses the classification and design considerations of hospitals, including classifications by level of care, size, medical specialists, and ownership.
2. It outlines the main divisions of hospitals including administration, outpatient, diagnostic services, therapeutic services, internal medical treatment, inpatient, and general services.
3. For each division and department, it describes the parts, location considerations, and provides area guidelines based on hospital size and international standards.
2012 03-07 home microbiome - gsc13 chinadansmith01
This document summarizes Daniel Smith's research on the interaction between human and home microbiomes. It discusses that humans carry 10 times more bacterial cells than human cells and that human health depends on microbiota. The research aims to monitor the microbiota of homes and their occupants over time using DNA sequencing of samples from body sites and household surfaces. Preliminary analysis of three homes shows variations in microbiota between body sites, surfaces within homes, and across different homes and occupants. Ongoing analysis will provide insights into how human and home microbiomes interact and influence each other.
Microbial interactions between humans and the built environment (Lake Arrowhe...Roxana Hickey
Presented by Roxana Hickey (Postdoctoral Scholar, Biology and the Built Environment Center, University of Oregon) at 21st Lake Arrowhead Microbial Genomics meeting (#LAMG16) in Lake Arrowhead, CA, on September 21, 2016
The document provides an introduction to key concepts in project management. It defines a project as a temporary endeavor to produce a unique product or service. It describes characteristics of projects like being temporary and unique. It then outlines various aspects of project management like the triple constraint of scope, time and cost. It discusses the role of a project manager in managing issues, risks, quality, scope and communication. Finally, it presents the typical project life cycle from initiation to closing.
Sample Prep Solutions for Microbiome ResearchQIAGEN
An accurate molecular analysis of the microbial constituents of a particular community is contingent upon high-yielding and non-biased nucleic acid extraction methodologies. Only by ensuring that all species and classes of microorganisms present in a sample are effectively lysed during extraction will one be able to reliably assess the composition of that sample. An additional challenge faced in nucleic acid extraction is the presence of persistent, co-purifying polymerase inhibitors endogenous to one’s sample. This presentation will focus on nucleic acid extraction tools developed by MO BIO Laboratories that facilitate accurate non-biased community analysis and eliminate common amplification problems via the depletion of endogenous polymerase inhibitors using our patented Inhibitor Removal Technology.
Microbiome Profiling with the Microbial Genomics Pro SuiteQIAGEN
In this slide deck, we introduce the scientist-friendly Microbial Genomics Pro Suite offering workflows optimized for microbiome profiling, microbial typing and outbreak analysis. The workflows and tools for microbial genomics introduced with this software package are further extending the comprehensive set of genomics, transcriptomics and epigenomics analysis solutions that researchers know from CLC Genomics Workbench.
Studies show that many projects either fail outright or fail to meet most of their objectives. There are a myriad of possible reasons why this might be the case. Very often, organizations go looking for a culprit and sometimes blame the project manager or even the very concept of project management itself. Sometimes they decide to “fix” the problem by getting all the project managers certified. Or they decide to standardize on a certain tool. And while certification and standardization are laudable things, they do not necessarily address the central problem or problems. This presentation will discuss the top ten reasons why projects fail and briefly discuss solutions to each problem. We will see how such areas as estimates, scope and “the accidental project manager” contribute to the problem.
There are three main project management structures: functional organization, dedicated project team, and matrix structure. In a functional organization, the project is managed within the existing functional hierarchy of the parent organization, providing flexibility but potentially slower responses. A dedicated project team operates independently as its own unit, keeping the team focused but being more expensive. A matrix structure combines functional and project management, allowing for resource sharing across projects but potentially causing tensions between managers.
Location and layout of hospital, need of hospital to community,planning,factors and data required in planning,fundamentals and objectives,principles,different stages,equipment planning,icu design and layout,quality quantity and temperature and noise control in hospital,conclusion
The Gulayan sa Paaralan Project (GPP) is a proposed project by the Department of Education to establish school gardens in Tagbina, Philippines. The objectives are to improve vegetable production and consumption, establish gardens as a food source for supplementary feeding, and showcase small-scale farming models. The project will target all elementary and secondary schools in Tagbina, benefiting over 24 elementary schools, 15 elementary schools, and 7 secondary schools. A budget of PHP 460,000 is requested, with PHP 391,000 from the national government and PHP 69,000 of local government counterpart funding. School administrators, teachers, parents, and officials will implement organic gardening with provided tools and seedlings.
QIAseq Technologies for Metagenomics and Microbiome NGS Library PrepQIAGEN
In this slide deck, learn about the innovative technologies that form the basis of QIAGEN’s portfolio of QIAseq library prep solutions for metagenomics and microbiome sequencing. Whether your research starts from single microbial cells, 16s rRNA PCR amplicons, or gDNA for whole genome analysis, QIAseq technologies offer tips and tricks for capturing the genomic diversity of your samples in the most unbiased, streamlined way possible.
The document provides guidance on writing a successful project proposal in 3 steps:
1. Plan the project by collaborating with stakeholders, developing a work plan and timeline, and drafting a concept paper and proposal.
2. Design the project using a conceptual model to identify problems, objectives, and interventions, and develop goals, objectives, activities, and indicators.
3. Write the proposal including an introduction, methodology, budget, monitoring and evaluation plan, sustainability discussion, checklist, and conclusion. Templates are provided for each section.
This is a final year project report on Ebola Virus Disease.....
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for more information and materials for the project contact me @ www.facebook.com/abhishekurmate
This document is a biology project on immunity submitted by Rahul Tripathi of class XII to his teacher Mr. Vikas Dixit. It contains an introduction, table of contents, chapters on the immune system including the fluid system, granulocytes, agranulocytes, lymphocytes, defense mechanisms, types of immunity like innate and adaptive immunity, and a conclusion thanking the teacher. The project aims to explain the key concepts of the immune system through chapters on its various components and functions to build understanding of how the body resists diseases.
1) A study investigated an outbreak of infections caused by a multidrug-resistant Klebsiella pneumoniae strain in an ICU between November and December 2000. 2) The outbreak was associated with contaminated roll boards used in operating rooms. 3) Active surveillance cultures identified 4 patients infected and 1 colonized with the outbreak strain within 2-18 days of surgery.
1) Nosocomial infections, also known as hospital-acquired infections, affect around 2 million patients per year in the US, resulting in around 90,000 deaths at a cost of $4.5-5.7 billion annually.
2) The most common sites of nosocomial infections are the urinary tract, surgical sites, bloodstream, and lungs for those on ventilators.
3) Prevention strategies aim to reduce the use and duration of invasive devices like urinary catheters when possible, as well as following strict insertion and maintenance protocols to minimize infection risks for those with necessary devices.
This document provides an outline of José Ramón Paño-Pardo's track at the ICAAC 2015 conference. The conference focused on antimicrobial agents and chemotherapy. Key topics included antimicrobial stewardship, bloodstream infections, new antimicrobials, and clinical infectious disease syndromes. Sessions covered emerging resistance issues like carbapenemase-producing Enterobacteriaceae and rapid diagnostics for sepsis.
This presentation is the gist of hospital infection control. Has touched all important policies and parameters involved in infection control in a healthcare settings in brief.
The purpose of this study was to investigate bacterial recovery and transfer from three biometric sensors and the survivability of bacteria on the devices. The modalities tested were fingerprint, hand geometry and hand vein recognition, all of which require sensor contact with the hand or fingers to collect the biometric. Each sensor was tested separately with two species of bacteria, Staphylococcus aureus and Escherichia coli. Survivability was investigated by sterilizing the sensor surface, applying a known volume of diluted bacterial culture to the sensor and allowing it to dry. Bacteria were recovered at 5, 20, 40 and 60 minutes after drying by touching the contaminated device with a sterile finger cot. The finger cot was re-suspended in 5 mL of saline solution, and plated dilutions to obtain live cells counts from the bacterial recovery. The transferability of bacteria from each device surface was investigated by touching the contaminated device and then touching a plate to transfer the bacteria to growth medium to obtain live cell counts. The time lapse between consecutive touches was one minute, with the number of touches was n = 50. Again, S. aureus and E. coli were used separately as detection organisms. This paper will describe the results of the study in terms of survival curves and transfer curves of each bacterial strain for each device.
The document summarizes a study that evaluated the ability of micropatterned surfaces to reduce bacterial transfer compared to unpatterned surfaces in a simulated clinical environment. Physician volunteers participated in a scenario where they encountered a mannequin inoculated with Staphylococcus aureus. Micropatterned or unpatterned films were placed on surfaces including a code cart, defibrillator button, and medication vial. Bacterial load was quantified from the surfaces. The micropatterned surfaces resulted in larger log reductions of bacteria compared to the unpatterned surfaces, demonstrating reduced bacterial transfer. Principal component analysis showed bacterial load was highly correlated between the code cart and defibrillator button. The micropatterned surfaces reduced bacterial
Advanced Next Generation DNA sequencing can more accurately diagnose infections by identifying bacteria, fungi, and viruses compared to traditional culture techniques. This allows for better treatment decisions. PathoGenius Laboratory uses Next Generation Sequencing to identify microbes in samples, providing physicians with diagnostic results to inform customized treatment. Previous methods of relying only on culture were found to significantly underrepresent the microbes present. Molecular diagnostic techniques provide more comprehensive information about biofilms and chronic infections compared to traditional approaches.
TOPIC: Control of Hospital Acquired Infections
المحاضر: أ.د. علي عبداللاه عبدالرحمن ( جامعة طيبه)
SPEAKER: prof. Ali A. Abdulrahman
(Prof. of microbiology & Immunology Taibah University)
TOPIC: Control of Hospital Acquired Infections
المحاضر: أ.د. علي عبداللاه عبدالرحمن ( جامعة طيبه)
SPEAKER: prof. Ali A. Abdulrahman
(Prof. of microbiology & Immunology Taibah University)
This document discusses a study that used next-generation DNA sequencing to analyze the microbiome of neuropathic diabetic foot ulcers. The study found that DNA sequencing identified more bacterial diversity in the ulcers than traditional cultures. DNA sequencing also showed higher microbial loads in the ulcers compared to cultures. This demonstrates that cultures underrepresent the true bacteria present in chronic wounds like diabetic foot ulcers. The study provides support for using molecular diagnostic approaches like DNA sequencing rather than solely relying on traditional cultures to identify bacteria in chronic wounds.
This document discusses the use of ultraviolet (UV) technology to disinfect surfaces and reduce the transmission of healthcare-associated infections (HAIs). It provides background on the risks of HAIs and the role of contaminated environmental surfaces in transmission. The document then describes how no-touch UV disinfection systems work to deactivate pathogens using UV-C light. Several studies are summarized that demonstrate the effectiveness of UV in reducing bacteria and spore counts on surfaces. The advantages and disadvantages of UV disinfection technology are also reviewed. Examples of several UV disinfection devices currently used in hospitals are provided.
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A Multifaceted Approach in Reducing Healthcare PathogensIFAH
Presentation by Dr. Christopher Truitt, Chief Science Officer, Infection Controls, Inc. at the Smart Health Conference 2018, held at Bally's Las Vegas on the 26-27th of April, 2018.
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This document discusses nosocomial or hospital-acquired infections. Some key points:
- Nosocomial infections are those that develop 48-72 hours or more after admission and were not present on admission.
- Major types include urinary tract infections, surgical site infections, pneumonia, and bloodstream infections.
- Risk factors include prolonged hospital stays, use of invasive devices like urinary catheters and IVs, and underlying patient conditions.
- Common pathogens vary by infection type but include Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella, E. coli, and Candida species. Many are resistant to antibiotics.
- Prevention strategies focus on hand hy
This document discusses advanced next-generation DNA sequencing techniques for identifying bacteria, fungi, and viruses. It highlights how DNA sequencing can identify over 13,000 pathogen DNA codes and is not affected by transport or culture issues. Examples are given where DNA sequencing identified chronic infections that cultures failed to detect. The document emphasizes how biofilms are difficult to culture but can be identified by DNA sequencing, and are responsible for 80% of infections. It provides examples comparing DNA sequencing to traditional cultures for identifying pathogens in chronic wounds and urine samples. The document also discusses using DNA diagnostic tests to provide treatment recommendations like customized topical therapies and antibiograms.
Hospital Infection Control focuses on preventing the spread of infections within hospitals through various practices and quality indicators. Some key areas of focus include hand hygiene, proper handling and disposal of biomedical waste, spill management, needlestick injury prevention, care of indwelling devices, surveillance of high-risk areas, sterilization processes, and monitoring of hospital-acquired infections. Standard precautions like proper use of personal protective equipment, isolation techniques, and barrier nursing help limit transmission between patients and staff.
This document provides information on a keyboard sterilization unit that uses UV light to eliminate bacteria, germs, and viruses from keyboards. It discusses the unit's design and how UV light works to sterilize surfaces. It also cites studies finding that keyboards harbor large numbers of bacteria and viruses and can spread illness. The document provides details on the product, market analysis, sales strategy, benefits for different sectors, and competitors.
This document discusses strategies to prevent hospital acquired infections (HAIs) such as ventilator-associated pneumonia (VAP) and hospital acquired pneumonia (HAP) at St. Joseph's University Medical Center. It defines different types of HAIs and provides statistics on their prevalence and impact. The document promotes adherence to prevention best practices like hand hygiene, oral care, and using closed suction systems. It emphasizes the role of all healthcare workers in implementing prevention measures to combat antibiotic-resistant infections and improve patient outcomes and safety.
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Breast cancer: Post menopausal endocrine therapyDr. Sumit KUMAR
Breast cancer in postmenopausal women with hormone receptor-positive (HR+) status is a common and complex condition that necessitates a multifaceted approach to management. HR+ breast cancer means that the cancer cells grow in response to hormones such as estrogen and progesterone. This subtype is prevalent among postmenopausal women and typically exhibits a more indolent course compared to other forms of breast cancer, which allows for a variety of treatment options.
Diagnosis and Staging
The diagnosis of HR+ breast cancer begins with clinical evaluation, imaging, and biopsy. Imaging modalities such as mammography, ultrasound, and MRI help in assessing the extent of the disease. Histopathological examination and immunohistochemical staining of the biopsy sample confirm the diagnosis and hormone receptor status by identifying the presence of estrogen receptors (ER) and progesterone receptors (PR) on the tumor cells.
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Treatment Options
Endocrine Therapy
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Selective Estrogen Receptor Modulators (SERMs): Tamoxifen is a SERM that binds to estrogen receptors, blocking estrogen from stimulating breast cancer cells. It is effective but may have side effects such as increased risk of endometrial cancer and thromboembolic events.
Aromatase Inhibitors (AIs): These drugs, including anastrozole, letrozole, and exemestane, lower estrogen levels by inhibiting the aromatase enzyme, which converts androgens to estrogen in peripheral tissues. AIs are generally preferred in postmenopausal women due to their efficacy and safety profile compared to tamoxifen.
Selective Estrogen Receptor Downregulators (SERDs): Fulvestrant is a SERD that degrades estrogen receptors and is used in cases where resistance to other endocrine therapies develops.
Combination Therapies
Combining endocrine therapy with other treatments enhances efficacy. Examples include:
Endocrine Therapy with CDK4/6 Inhibitors: Palbociclib, ribociclib, and abemaciclib are CDK4/6 inhibitors that, when combined with endocrine therapy, significantly improve progression-free survival in advanced HR+ breast cancer.
Endocrine Therapy with mTOR Inhibitors: Everolimus, an mTOR inhibitor, can be added to endocrine therapy for patients who have developed resistance to aromatase inhibitors.
Chemotherapy
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1. The Hospital Microbiome Project:
Experimental Designs for Investigating the
Development of Microbial Communities
Daniel Patrick Smith
Hospital Microbiome Workshop
University of Chicago, 6.7.2012
2. Background
How microbial communities
persist and change in indoor
environments is of immense
interest to public health
bodies and scientists.
Demographics of a building
play a key role in shaping
microbial communities.
– Humans aerosolize up to 37
million bacteria per person-
hour (Qian, 2012)
– Forensic microbiology can
determine who last touched
an object by their
microbiota. (Fierer, 2010)
Qian, J., Hospodsky, D., Yamamoto, N., Nazaroff, W. W. & Peccia, J. Indoor Air (2012).
Fisk, W. J. Annual Review of Energy and the Environment 25, 537–566 (2000).
Fierer, N. et al. Proceedings of the National Academy of Sciences 107, 6477–6481 (2010).
3. Background:
Hospitals as a Sampling Site
A newly constructed hospital
presents the ideal conditions for
studying the development of
bacterial communities driven by
human demographics.
– Patient rooms are identically
constructed – replicates.
– Building materials are defined.
– Closed environment.
– No prior pathogenic contamination.
– Relevant microorganisms are
thoroughly characterized.
Hospital Microbiome Workshop
4. Background:
Hospital Acquired Infections (HAI)
The ten most common pathogens:
– coagulase-negative staphylococci
– Staphylococcus aureus
– Enterococcus species
– Candida species
– Escherichia coli Accounted for 84% of
– Pseudomonas aeruginosa the observed HAIs in
– Klebsiella pneumoniae 463 hospitals over a
– Enterobacter species 21 month period.
– Acinetobacter baumannii (Hidron, 2008)
– Klebsiella oxytoca
Hidron, A. I. et al. Infection Control and Hospital Epidemiology 29, 996–1011 (2008).
5. Background:
Hospital vs. Non-Hospital Infections
Contracted Fatal (% Fatal)
Hospital 1.7 million 99,000 (6%)
Non-Hospital 1.5 million 15,743 (1%)
Cause of Death – Total over U.S. in 2002 Number
1. Diseases of heart 696,947
2. Malignant neoplasms 557,271
4.5 Infections per 3. Cerebrovascular diseases 162,672
100 Hospital admissions 4. Chronic lower respiratory diseases 124,816
5. Accidents (unintentional injuries) 106,742
Hospital Acquired Infection - associated 99,000
6. Diabetes mellitus 73,249
7. Influenza and pneumonia 65,681
8. Alzheimer’s disease 58,866
Groseclose SL, et al. (2004) MMWR Morb Mortal Wkly Rep 51: 1–84. Anderson RN, Smith BL (2005) Natl Vital Stat Rep 53: 1–89.
Hall-Baker PA, et al. (2010) MMWR Morb Mortal Wkly Rep 57: 1–100. Klevens RM, et al. (2007) Public Health Rep 122: 160–166.
6. Project Goal
Determine which environmental parameters have the
greatest influence on the development of microbial
communities within a hospital.
– Patient/Staff Microflora – Light Level/Source
– Building Material – Demographic Exposure
– Temperature/Humidity • High vs Low Traffic
• Staff vs Patient Area
Understand how demographics interact with the
succession of microorganisms in a hospital.
Hospital Microbiome Workshop
7. Guiding Hypotheses
1. Microbial community structure on hospital surfaces can be predicted by
human demographics, physical conditions (e.g. humidity, temperature),
and building materials for each location and time.
2. A patient-room microbiota is influenced by the current patient and
their duration of occupancy, and shows community succession with the
introduction of a new occupant.
3. The colonization of the surfaces and patients by potential pathogens is
influenced by composition and diversity of the existing microbial
community derived from previous occupants of the space.
4. The rate of microbial succession is driven by demographic usage and
building materials.
Hospital Microbiome Workshop
8. Ideal Sampling Strategy:
Daily Sampling of Bacterial Reservoirs for a Year.
Patient Area Water Travel Areas
Bed rails, tray table, call boxes, Cold tap water, hot tap water, Corridor floor & wall, stairwell
telephone, bedside tables, water used to clean floors. handrail & steps & door knobs
patient chair, IV pole, floor, & kick plates, elevator buttons
light switches, air exhaust. Patient & floor & handrail.
Stool sample, nasal swab, hand.
Patient Restroom Lobby
Sink, light switches, door knob, Staff Front desk surface, chairs,
handrails, toilet seats, flush coffee tables, floor.
lever, bed pan cleaning Nasal swab, bottom of shoe,
equipment, floor. dominant hand, cell phone,
computer mouse, work phone, Public Restroom
shirt cuff, stethoscope. Floor, door handles, sink
Additional Equipment controls, sink bowl, soap
IV Pump control panel, monitor 240 Patient Rooms + 50 Staff dispenser, towel dispenser,
control panel, monitor touch = 2,437,105 samples toilet seats, toilet lever, stall
screen, monitor cables, = $24 million in extraction & door lock, stall door handle,
ventilator control panel. sequencing consumables alone urinal flush lever.
Hospital Microbiome Workshop
9. Reduced Sampling Strategy:
Weekly Sampling for a Year of 187 Sites
Human Patient Room (x20) Nurse Station (x1)
Patients (≤ 20) Floor Countertop
– Nose Bedrail Computer mouse
– Stool IV control panel Phone handle
Staff (x5) Faucet handle Chair
– Nose Outer door handle Corridor floor
– Uniform cuff
Air exhaust filter Hot tap water
– Pen
Cold tap water
– Cell phone
Hospital Microbiome Workshop
10. Sampling Airborne Microorganisms
Each patient room has independent exhaust vents which can
be fitted with removable filters for this study.
– Replace filters weekly.
– Use ventilation rate, filter efficiency, and microbial abundance to
calculate the concentration of airborne microorganisms.
Further interrogation via particle
deposition onto blood-agar plates
for a 1 hr period, followed by
challenging of colonies with
antibiotic susceptibility tests.
Hospital Microbiome Workshop
11. Sampling Protocol:
Compatible with Quantitative Analyses
Sterile swabs moistened with saline solution will be used to
sample a region of pre-defined dimensions.
– qRT-PCR provides an estimate of genomes, yielding cells/cm2
– Allows conclusions to be drawn regarding actual abundance of
microbial taxa, rather than relative abundance.
Hot and cold water supplies
– Single location
– Run for 15 sec
– Extract from 100 uL
Hospital Microbiome Workshop
12. Sample Selection
Although 20 patient rooms and their occupants will be
sampled, only 8 will be selected for sequencing.
– Dramatically reduces expenses for sample prep & sequencing.
– 4 rooms in which HAIs were contracted.
– 4 rooms in which HAIs were NOT contracted.
Addresses the hypothesis:
The colonization of the surfaces and patients by potential pathogens is
influenced by composition and diversity of the existing microbial
community derived from previous occupants of the space.
Hospital Microbiome Workshop
13. Passive Monitoring
Data loggers will be placed in patient
rooms to take hourly measurements of:
– Temperature
– Relative Humidity
– Dew Point
National Oceanic and Atmospheric
Administration records will be used to
obtain data on outdoor environmental
conditions.
Hospital Microbiome Workshop
14. Patient Infections
We will request IRB approval for accessing pathogen reports
for patients participating in this study if they contract, or are
admitted with, an infection.
Hospital Microbiome Workshop
15. Project Timeline
November 2012
– Conduct survey of building materials.
– Identify all sampling locations in the building, and begin collecting
surface, air, and water samples.
– Secure and activate data loggers in patient rooms.
December 2012
– Identify staff members who wish to participate and begin sampling
them in their current working environment.
January 31st, 2013 – Hospital Opens
– Identify patients who wish to participate and begin sampling them a
they are admitted to the rooms under obervation.
Hospital Microbiome Workshop
16. Sample Processing
Swab tips are cut off and placed in a lysis/PCR solution.
After incubation and thorough mixing, aliquots are
distributed to 96-well PCR plates in triplicate.
Amplification of 16S/18S/ITS takes place in a qualitative real
time (qRT) PCR machine using barcoded primers.
Samples are pooled into groups of 500 and sequenced to a
depth of 3,000 read pairs (2 x 150 bp) per sample.
Reads are filtered for quality, merged into 250 bp reads, and
demultiplexed based on barcode.
Hospital Microbiome Workshop
17. Data Analysis
The QIIME software suite will be used to:
– Cluster reads into operational taxonomic units (OTUs).
– Phylogenetically classify OTUs based on reference databases.
– Calculate alpha and beta diversity among samples.
– Visualize sample similarity via principle coordinate analysis plots.
Caporaso, J. G. et al. Nature Methods 7, 335-336 (2010).
18. Data Analysis
SourceTracker will be used to:
– Identify sources and proportions of contamination on surfaces.
– Answer questions such as “What proportion of the air’s microbes
originate from a patient’s nasal microbiome?”
Knights, D. et al. Nature Methods 8, 761-763 (2011).
19. Data Analysis
Microbial Assemblage Prediction (MAP) will be used to:
– Predict the relative abundance of microorganisms in an
environment, given set of environmental conditions.
– Simulate how community composition will shift if an environmental
variable is altered.
Env. Parameter
Rhodobacteriales
Flavobacteriales
Rickettsiales
Pseudomonadales
Opitutales
Vibrionales
Rhizobiales
Larsen, P. E., Field, D. & Gilbert, J. A. Nature Methods (2012).
20. Data Analysis
Local Similarity Analysis will be used to:
– Identify patterns in microbial succession. E.g. if organism A is
blooming now, then organism B will bloom in a few weeks.
Gilbert, J. A. et al. The ISME Journal 6, 298-308 (2011).
21. Project Scope
We are currently pursing a grant that will enable processing
of 4,732 samples collected over 52 weeks from 91 locations:
Human Patient Room (x8) Nurse Station (x1)
Patients (≤ 8) Floor Countertop
– Nose Bedrail Computer mouse
– Stool IV control panel Phone handle
Staff (x5) Faucet handle Chair
– Nose Outer door handle Corridor floor
– Uniform cuff
Air exhaust filter Hot tap water
– Pen
– Cell phone Cold tap water
Additional funding could allow for:
– More frequent collection – Increased replication
– Additional sampling locations – Introduction of variables
– Longer time-course • Cancer vs. surgery wards
• North vs. south facing windows
Hospital Microbiome Workshop