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.
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.
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 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 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 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.
1. Whole genome sequencing is becoming more affordable and widespread, allowing for large datasets and personalized medicine applications.
2. However, genomic data is extremely sensitive and can be used to identify individuals and their relatives, even when anonymized. Once a genome is leaked, it cannot be revoked.
3. Computer scientists are exploring techniques to protect genomic privacy, such as differential privacy and secure computation, but enabling privacy-preserving genomic research remains a challenge.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
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.
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.
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 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 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 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.
1. Whole genome sequencing is becoming more affordable and widespread, allowing for large datasets and personalized medicine applications.
2. However, genomic data is extremely sensitive and can be used to identify individuals and their relatives, even when anonymized. Once a genome is leaked, it cannot be revoked.
3. Computer scientists are exploring techniques to protect genomic privacy, such as differential privacy and secure computation, but enabling privacy-preserving genomic research remains a challenge.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
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.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...nist-spin
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
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 document discusses the gut microbiota. It states that the gut contains trillions of microbes including bacteria, archaea, fungi and viruses. These microbes help digest food, harvest energy, regulate the immune system and prevent diseases like IBS and cancer. Techniques to study the gut microbiota include culturing, PCR, fluorescence in situ hybridization and direct sequencing of the 16S rRNA gene. Pyrosequencing provides high throughput sequencing of the 16S rRNA gene and allows identification of unknown bacterial species. Stool samples are commonly used to study the gut microbiota as they are easier to collect than biopsy samples.
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.
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.
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: 2.1.3- 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.
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
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.
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.
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.
Biochemistry: A pivotal aspects in forensic scienceVanshikaVarshney5
In the above presentation, you will know the importance of biochemistry in forensic science. Biochemistry is not all about the chemicals, it is about your life, your environment. Basically, it belongs to you.
in this presentation, you can know about the biochemical techniques which are majority used in forensic science and various research occurs in the field of forensic science which is related with biochemistry.
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: 2.1.2- 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.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Added Value of Open data sharing using examples from GenomeTrakrExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Added Value of Open data sharing using examples from GenomeTrakr. 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.
"Bacterial Pathogen Genomics at NCBI" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Dr. Bill Klimke.
Nothing in Microbiology makes Sense except in the Light of EvolutionMark Pallen
Professor Mark Pallen's Inaugural Lecture at Warwick Medical School, University of Warwick, April 15th 2014.
Storified version of lecture: https://storify.com/mjpallen/palleninaugural
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.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...nist-spin
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
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 document discusses the gut microbiota. It states that the gut contains trillions of microbes including bacteria, archaea, fungi and viruses. These microbes help digest food, harvest energy, regulate the immune system and prevent diseases like IBS and cancer. Techniques to study the gut microbiota include culturing, PCR, fluorescence in situ hybridization and direct sequencing of the 16S rRNA gene. Pyrosequencing provides high throughput sequencing of the 16S rRNA gene and allows identification of unknown bacterial species. Stool samples are commonly used to study the gut microbiota as they are easier to collect than biopsy samples.
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.
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.
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: 2.1.3- 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.
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
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.
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.
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.
Biochemistry: A pivotal aspects in forensic scienceVanshikaVarshney5
In the above presentation, you will know the importance of biochemistry in forensic science. Biochemistry is not all about the chemicals, it is about your life, your environment. Basically, it belongs to you.
in this presentation, you can know about the biochemical techniques which are majority used in forensic science and various research occurs in the field of forensic science which is related with biochemistry.
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: 2.1.2- 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.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Added Value of Open data sharing using examples from GenomeTrakrExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Added Value of Open data sharing using examples from GenomeTrakr. 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.
"Bacterial Pathogen Genomics at NCBI" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Dr. Bill Klimke.
Nothing in Microbiology makes Sense except in the Light of EvolutionMark Pallen
Professor Mark Pallen's Inaugural Lecture at Warwick Medical School, University of Warwick, April 15th 2014.
Storified version of lecture: https://storify.com/mjpallen/palleninaugural
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
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)
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.
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.
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 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
1. Hospital-acquired infections can occur due to susceptible patients, the hospital environment, diagnostic and therapeutic procedures, and multi-drug resistant pathogens. Common sites of infection include the urinary tract, respiratory tract, wounds, bloodstream, and gastrointestinal tract.
2. Infections can spread through direct contact, airborne transmission, the oral route from contaminated food or fluids, or parenterally through blood or intravenous lines. Proper hand hygiene, sterilization of medical equipment, isolation of infected patients, and judicious antibiotic use are important for controlling the spread of infection.
3. Effective hospital infection control committees oversee surveillance, outbreak management, antibiotic stewardship, and environmental cleaning policies to minimize healthcare
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.
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.
A newly invented antibacterial in decontamination of reusable hospital a deviceAlexander Decker
This document describes a study that tested the effectiveness of a newly invented antibacterial solution for decontaminating reusable medical devices. 18 used medical devices were collected from an intensive care unit and decontaminated using different concentrations and contact times of Sidr tree leaf extract, hydrogen peroxide, and their combination. Mixing 62.5 g/L Sidr extract with 1.5% hydrogen peroxide was found to effectively eradicate contamination from the devices after 30 minutes of contact. The new antibacterial agent shows potential for decontaminating reusable medical equipment through its ability to eliminate bacteria from contaminated devices within 30 minutes.
A newly invented antibacterial in decontamination of reusable hospital a deviceAlexander Decker
This document describes a study that tested the effectiveness of a newly invented antibacterial solution for decontaminating reusable medical devices. 18 used medical devices were collected from an intensive care unit and decontaminated using different concentrations and contact times of Sidr tree leaf extract, hydrogen peroxide, and their combination. Mixing 62.5 g/L Sidr extract with 1.5% hydrogen peroxide was found to effectively eradicate contamination from the devices after 30 minutes of contact. The new antibacterial agent shows potential for decontaminating reusable medical equipment.
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 summarizes an investigation into an outbreak of Burkholderia cepacia infections caused by drug contamination at a hospital in China. Samples were taken from the hospital environment, medical instruments, and unopened drugs. Burkholderia cepacia was isolated from surgical instruments and two batches of analgesic gel. Pulsed-field gel electrophoresis showed that bacteria isolated from patients and the contaminated analgesic gel were homologous, confirming the outbreak. The outbreak was likely caused by water pollution during drug production or defects allowing improper disinfection.
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.
The document discusses hospital acquired infections, also known as nosocomial infections. It defines nosocomial infections as infections acquired during or after hospitalization. It discusses the epidemiological interaction between host factors, infectious agents, and the hospital environment. It also summarizes common bacterial, viral, and fungal agents that cause nosocomial infections and how they are transmitted. Prevention and control methods like isolation precautions, hand hygiene, and surveillance programs are also outlined.
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.
Similar to Jan 15 2013 Hospital Microbiome Meeting (20)
1. The Hospital Microbiome Project:
Experimental Designs for Investigating the
Development of Microbial Communities
Daniel Patrick Smith
Hospital Microbiome Workshop
University of Chicago, 1.15.2013
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 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.
5. 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).
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
– Airflow rate • Staff vs Patient Area
– Cleaning practices – Prior Room Occupants
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. Implemented Sampling Strategy:
Daily/Weekly Sampling for a Year of 142 Sites
Human Patient Room (x10) Nurse Station (x2)
Patients (≤ 10) Floor Countertop
– Nose Bedrail Computer mouse
– Hand Cold tap water Phone handle
– Inguinal Fold Glove box Chair
Staff (x8) Air exhaust filter Corridor floor
– Nose
Hot tap water
– Hand
Cold tap water
– Uniform cuff
– Pager
– Cell phone
– Shoe
Hospital Microbiome Workshop
10. Sampling Airborne Microorganisms
Each patient room has independent exhaust vents which can
be fitted with removable filters for this study.
– Sterilize filter media with autoclaving and UV-exposure
– Replace filters daily/weekly.
– Use ventilation rate, filter efficiency, and microbial abundance to
calculate the concentration of airborne microorganisms.
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
– Sample hot & cold water at nurse
stations on 9th & 10th floors
– Patient room cold tap
– Run for 15 sec
– Absorb onto swab
Hospital Microbiome Workshop
12. Sample Selection
Ten patient rooms and their occupants will be sampled
– Two rooms: Sample every day.
– Eight additional rooms: Sample weekly.
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. Antibiotic Effects on Patient Microflora
Antibiotics dramatically alter the natural microflora of
humans. We will be able to monitor the effect of several
antibiotic regimens on the skin, nasal, and inguinal fold
microbiomes of the subjects in this study.
Hospital Microbiome Workshop
14. Project Timeline
January 2013
– Identify all sampling locations in the building
– Begin collecting surface, air, and water samples.
– Secure and activate data loggers in patient rooms.
February 2013
– Identify staff members who wish to participate and begin sampling
them in their current working environment.
February 23rd, 2013 – Hospital Opens
– Identify patients who wish to participate and begin sampling them a
they are admitted to the rooms under observation.
January 2014
– Conduct chart reviews after completion of sample collection phase.
Hospital Microbiome Workshop
15. 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
16. 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).
17. 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).
18. 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).
19. 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).