Legionella Laboratory Testing | Biosan Laboratories
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With increasing legionella contamination in Michigan-based businesses, it has become necessary for all commercial and residential properties in the state to opt for legionella laboratory testing from a reliable microbiological laboratory. For More Details Visit: http://www.biosan.com/
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SteilLinkedInResume2015
Benjamin P. Steil has over 15 years of experience in virology research. He received his Ph.D. in Microbiology and Immunology from the University of Colorado Denver in 2008, and has since worked as a postdoctoral fellow and staff scientist developing viral vaccine adjuvants. His skills include viral particle production, nucleic acid techniques, mouse models, and immunological assays. Currently he is seeking a position where he can apply his expertise in vaccine design and development.
Flyer Cleanpid Easy Purification Kit
Flyer of our new product Cleanpid® Easy Purification Kit for detecting Legionella. Cleanpid is for purification the sample before doing the PCR. After using CLEANPID you can collect the Legionella cells and with freeze/thaw cycles you can obtain the DNA and with PCR, the customer could say if there is or not Legionella presence.
Legionellae DNA extraction is particularly problematic when different types of microorganisms may be present.
Cleanpid® Easy Purification kit is the simple method for the separation and purification of Legionella in water samples. The method is based on Legionella binding magnetic beads for capturing cells (immunomagnetic separation).
No columns or centrifugations are necessary.
A summary of the advantages of Cleanpid is:
Quick and Easy-To-Use
The kit only requires a magnetic rack (we provide it)
Improves the sensitivity and reproducibility of qPCR
Reduction of false positive rate for PCR:
o Detects only legionella viable cells (not exogenous DNA, not other microbiota...)
Reduction of false negative rate for PCR:
o Obtains a larger amount of DNA from the water samples (avoid dilution of the DNA samples for eliminating inhibitors)
The purified organism is additionally suitable for DNA extraction by simply freeze/thaw cycles (simply and cost-efficient lysis)
http://www.biotica.es/en/Products/Cleanpid%20Easy%20Purification%20kit%20for%20Legionella
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The document discusses using metagenomics and metaproteomics to examine the presence and diversity of polysaccharide-degrading microorganisms that colonize baits in situ. It describes using an integrated 'omic' approach including metagenomics, metaproteomics, stable isotope probing, and isolation to characterize the microorganisms. It also discusses challenges in protein database searches and modular enzymes, and solutions for probing polysaccharide-degrading enzymes including a Perl script to download protein domain accessions and trim sequences.
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This document describes the production of Short Chain Variable Fragments (ScFv) that specifically bind to E. coli for use in detecting E. coli in water samples. Chickens were immunized with bacterial glycoconjugates to produce antibodies. RNA from the chickens was used to generate a ScFv gene library displayed on phages. ScFvs that bound strongly to E. coli were isolated through biopanning. The purified phage was used to produce soluble ScFv in E. coli for assessment of binding specificity to E. coli and Enterobacter cloacae via dot blot analysis. The ScFv showed strong binding to E. coli samples and negligible binding to E. cloacae, indicating potential for use
Forensic Identification using skin bacterial communities
This study aimed to determine if the unique bacterial communities that reside on human skin could be used for forensic identification. The researchers found that the bacterial communities on individuals' hands were distinct and persisted for days on surfaces they touched. DNA analysis of bacteria collected from keyboards, mice, and skin swabs was able to match the bacteria to the correct individuals at a rate better than chance. This suggests the potential for bacterial fingerprinting to identify individuals who have touched objects, but more research is still needed to establish the technique for use in forensics.
Rapid Legionella PCR test
Legionnaires' disease, caused by Legionella bacteria found in water systems, infects 300-400 people annually in England and Wales. A recent European study tested a new quantitative PCR method for rapidly detecting Legionella in water samples, finding results within hours rather than the 2 weeks needed for traditional culture methods. The study concluded that action levels could be set based on qPCR results, allowing facilities to take remedial action sooner. A UK hospital is now planning to adopt the qPCR method to supplement or replace culture testing for Legionella monitoring in water systems.
APPLICATION OF PCR IN MEDICAL MICROBIOLOGY
For over 10 decades, agents of infectious diseases have been identified through their phenotype directly in specimen and after a growth in culture.
Today, we are in a molecular era, there is an opportunity to detect organisms more rapidly and accurately based on their genetic signatures.
Biomedical science research discovery offers a growing numbers of a nucleic acid amplification tests (NAATS) among which is polymerase chain reaction (PCR) for detection and identification of bacterial, parasitic, fungi and viral pathogens.
These assays improve patient care, reduce antibiotic usage, enhance test utilization and increase laboratory and hospital efficiency.
In this seminar, we will explore the clinical usefulness and potential of both conventional and real-time PCR assays in Clinical Microbiology.
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Recommended
SteilLinkedInResume2015
Benjamin P. Steil has over 15 years of experience in virology research. He received his Ph.D. in Microbiology and Immunology from the University of Colorado Denver in 2008, and has since worked as a postdoctoral fellow and staff scientist developing viral vaccine adjuvants. His skills include viral particle production, nucleic acid techniques, mouse models, and immunological assays. Currently he is seeking a position where he can apply his expertise in vaccine design and development.
Flyer Cleanpid Easy Purification Kit
Flyer of our new product Cleanpid® Easy Purification Kit for detecting Legionella. Cleanpid is for purification the sample before doing the PCR. After using CLEANPID you can collect the Legionella cells and with freeze/thaw cycles you can obtain the DNA and with PCR, the customer could say if there is or not Legionella presence.
Legionellae DNA extraction is particularly problematic when different types of microorganisms may be present.
Cleanpid® Easy Purification kit is the simple method for the separation and purification of Legionella in water samples. The method is based on Legionella binding magnetic beads for capturing cells (immunomagnetic separation).
No columns or centrifugations are necessary.
A summary of the advantages of Cleanpid is:
Quick and Easy-To-Use
The kit only requires a magnetic rack (we provide it)
Improves the sensitivity and reproducibility of qPCR
Reduction of false positive rate for PCR:
o Detects only legionella viable cells (not exogenous DNA, not other microbiota...)
Reduction of false negative rate for PCR:
o Obtains a larger amount of DNA from the water samples (avoid dilution of the DNA samples for eliminating inhibitors)
The purified organism is additionally suitable for DNA extraction by simply freeze/thaw cycles (simply and cost-efficient lysis)
http://www.biotica.es/en/Products/Cleanpid%20Easy%20Purification%20kit%20for%20Legionella
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The document discusses using metagenomics and metaproteomics to examine the presence and diversity of polysaccharide-degrading microorganisms that colonize baits in situ. It describes using an integrated 'omic' approach including metagenomics, metaproteomics, stable isotope probing, and isolation to characterize the microorganisms. It also discusses challenges in protein database searches and modular enzymes, and solutions for probing polysaccharide-degrading enzymes including a Perl script to download protein domain accessions and trim sequences.
4th Year Project
This document describes the production of Short Chain Variable Fragments (ScFv) that specifically bind to E. coli for use in detecting E. coli in water samples. Chickens were immunized with bacterial glycoconjugates to produce antibodies. RNA from the chickens was used to generate a ScFv gene library displayed on phages. ScFvs that bound strongly to E. coli were isolated through biopanning. The purified phage was used to produce soluble ScFv in E. coli for assessment of binding specificity to E. coli and Enterobacter cloacae via dot blot analysis. The ScFv showed strong binding to E. coli samples and negligible binding to E. cloacae, indicating potential for use
Forensic Identification using skin bacterial communities
This study aimed to determine if the unique bacterial communities that reside on human skin could be used for forensic identification. The researchers found that the bacterial communities on individuals' hands were distinct and persisted for days on surfaces they touched. DNA analysis of bacteria collected from keyboards, mice, and skin swabs was able to match the bacteria to the correct individuals at a rate better than chance. This suggests the potential for bacterial fingerprinting to identify individuals who have touched objects, but more research is still needed to establish the technique for use in forensics.
Rapid Legionella PCR test
Legionnaires' disease, caused by Legionella bacteria found in water systems, infects 300-400 people annually in England and Wales. A recent European study tested a new quantitative PCR method for rapidly detecting Legionella in water samples, finding results within hours rather than the 2 weeks needed for traditional culture methods. The study concluded that action levels could be set based on qPCR results, allowing facilities to take remedial action sooner. A UK hospital is now planning to adopt the qPCR method to supplement or replace culture testing for Legionella monitoring in water systems.
APPLICATION OF PCR IN MEDICAL MICROBIOLOGY
For over 10 decades, agents of infectious diseases have been identified through their phenotype directly in specimen and after a growth in culture.
Today, we are in a molecular era, there is an opportunity to detect organisms more rapidly and accurately based on their genetic signatures.
Biomedical science research discovery offers a growing numbers of a nucleic acid amplification tests (NAATS) among which is polymerase chain reaction (PCR) for detection and identification of bacterial, parasitic, fungi and viral pathogens.
These assays improve patient care, reduce antibiotic usage, enhance test utilization and increase laboratory and hospital efficiency.
In this seminar, we will explore the clinical usefulness and potential of both conventional and real-time PCR assays in Clinical Microbiology.
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Design and Evaluation of a 16S-based Integrated Solution to Study Bacterial D...
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Analysis of 16S sequences in microbial population gives a quick
overview of the community diversity, and is usually performed by
sequencing one or two hypervariable regions (V-regions), amplified as
a single PCR fragment. We developed a novel approach that
simultaneously surveys multiple V-regions in the 16S rRNA gene.
In the first design of PCR primer pools, V-regions 2, 3, 4, 6-7, 8 and 9
were amplified as individual ~200 bp fragments in one of two multiplex
PCR reactions. The primer pools covered more than 80% of
eubacterial sequences in the GreenGenes database with perfectly
matched primer pairs for at least one V-region. In the second design
the amplicons are longer, 300-400 bp products
Our data analysis module classified individual reads by mapping them
to the reference libraries. With the fragment sizes ranging between
200-300 bp, we achieved genus and, in many cases species level
taxonomic resolution, depending on which V-region was evaluated.
In an initial evaluation we tested the complete solution (PCR
chemistry, workflow and software) on two mock community DNA
samples from BEI resources: HM-276D - even community, with equal
number of rDNA copies for each of 20 bacteria and HM-783D–
staggered community, with variable number of rDNA copies. Several
V-regions were amplified by our primer sets for every organism in the
mock community. The number of classified reads in each V-region for
every bacteria depended on both primer complementarity and ease of
sequencing of the particular PCR fragment. Our approach of
interrogating multiple V-regions and sequencing both amplicon strands
improved system robustness against both PCR and sequencing
biases.
The 314v2 chip achieved 1:100 sensitivity (detection of all organisms
in the staggered mock community with 10^4-10^6 rDNA copies/PCR).
Increased sequencing depth (316v2 and 318v2) increased sensitivity
to 1:1000 (10^3-10^6 rDNA copies).
With human samples, we observed no PCR cross-reactivity with
human DNA and were able to identify and determine characteristic Vsignatures
of several important species. The signatures not only help
to increase the confidence in the organism presence and ID, but may
potentially enable strain differentiation.
Survey of multiple V-regions is useful in monitoring changes in the
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Furthermore, some species are not easily culturable. We
have developed a facile research method for identifying
bacterial species by 16S ribosomal RNA sequencing on the
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designed to PCR amplify the hypervariable regions of the 16S
gene of bacteria. We used this kit to construct libraries from
15 retrospective samples of synovial fluid with various
bacterial species either spiked in or present at collection.
Libraries were sequenced on the Ion PGM™ system and the
data analysis performed using the Ion Reporter™ workflow
which provides an automated analysis solution. Bacteria
present in the samples were correctly identified in samples
containing a single spiked-in species, mixed-species samples,
and in infected samples. Thus, the Ion Torrent™ platform
provides a mechanism for rapidly identifying bacteria that are
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1) Clonal culturing of microorganisms within emulsion droplets, which allows culturing of microbes that do not form colonies and collection of target droplets.
2) Genetic screening for high functional proteins using emulsion droplets containing both genetic information and expressed proteins, enabling isolation based on protein activity.
3) Digital PCR within emulsion droplets to quantify nucleic acids and selectively recover droplets with fluorescence, applicable to screening cells with specific mutations.
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1) The study constructed five cDNA libraries from the vine mealybug, Planococcus ficus, to obtain genetic sequence data for the pest. An RNA extraction protocol was optimized to obtain high quality RNA from the mealybugs.
2) The primary library contained many short inserts, while the fractionated libraries contained size-selected inserts ranging from ~0.25kb to 4kb.
3) A pilot analysis found that 41% of sequences matched databases, mostly being of insect origin. Two potential RNAi targets for mealybug control were identified and seemed unique to arthropods.
Automated system for bacterial identification
[DOWNLOAD IT OPEN IT WITH MICROSOFT POWERPOINT THEN YOU WILL BE ABLE TO UNDERSTAND THE TOPIC COVERED.]
1. WHOLE TEXT IS RELIABLE.
2. TEXT HAS BEEN TAKEN FROM STANDARD TEXT BOOK FOR MEDICAL MICROBIOLOGY.
3. SOME PICTURE HAS BEEN TAKEN FROM JOURNAL.
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- The authors integrated an ADE system into their workflow for PCR and qPCR reactions, allowing analysis of complex genetic models. ADE increased throughput by 8-10x compared to traditional robots.
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3rd International Conference on Bio-Sensing Technology 2013
This work won the Award for Outstanding Oral Presentation at the 3rd International Conference on Bio-Sensing Technology 2013.
Pierre R. Marcoux, Mathieu Dupoy
Department of Technology for Biology and Healthcare, CEA-LETI MINATEC, 17 avenue des Martyrs, 38054 Grenoble, France.
Antoine Cuer, Joe-Loïc Kodja, Arthur Lefebvre, Florian Licari, Robin Louvet, Anil Narassiguin
These authors contributed equally to this work.
Ecole Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France.
Frédéric Mallard
bioMérieux SA, Innovation & Systems / Technology Research / Sample Prep & Processing Lab, 5 rue des Berges, 38000 Grenoble, France.
The development of methods for the rapid identification of pathogenic bacteria is a major step towards accelerated clinical diagnosis of infectious diseases and efficient food and water safety control. Methods for identification of bacterial colonies on gelified nutrient broth have the potential to bring an attractive solution, combining simple optical instrumentation, no need for sample preparation or labelling, in a non-destructive process. Here, we studied the possibility of discriminating different bacterial species at a very early stage of growth (6 hours of incubation at 37°C), on thin layers of agar media (1mm of Tryptic Soy Agar), using light forward-scattering and learning algorithms (Bayes Network, Continuous Naive Bayes, Sequential Minimal Optimisation). A first database of more than 1000 scatterograms acquired on seven Gram-negative strains yielded a recognition rate of nearly 80%, after only 6 hours of incubation. We investigated also the prospect of identifying different strains from a same species through forward scattering. We discriminated thus four strains of Escherichia coli with a recognition rate reaching 82%. Finally, we show the discrimination of two species of coagulase-negative Staphylococci (S. haemolyticus and S. cohnii), on a commercial selective pre-poured medium used in clinical diagnosis (ChromID MRSA, bioMérieux), without opening lids during the scatterogram acquisition. This shows the potential of this method – non-invasive, preventing cross-contaminations and requiring minimal dish handling – to provide early clinically-relevant information in the context of fully automated microbiology labs.
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3) While powerful, 16S rRNA sequencing has some limitations like requiring a pure culture and difficulty differentiating closely related species, and interpretation requires consideration of database issues.
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This document discusses molecular microbiology and some of its techniques. It begins by defining molecular microbiology as the study of the molecular basis of physiological processes in microorganisms and manipulation of DNA. It then discusses several molecular techniques used, including polymerase chain reaction (PCR) and its applications such as quantitative real-time PCR and multiplex PCR. The document also discusses uses of molecular microbiology such as detection of pathogens and its role in fields like environmental microbiology.
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Design and Evaluation of a 16S-based Integrated Solution to Study Bacterial D...
Design and Evaluation of a 16S-based Integrated Solution to Study Bacterial D...Thermo Fisher Scientific
Analysis of 16S sequences in microbial population gives a quick
overview of the community diversity, and is usually performed by
sequencing one or two hypervariable regions (V-regions), amplified as
a single PCR fragment. We developed a novel approach that
simultaneously surveys multiple V-regions in the 16S rRNA gene.
In the first design of PCR primer pools, V-regions 2, 3, 4, 6-7, 8 and 9
were amplified as individual ~200 bp fragments in one of two multiplex
PCR reactions. The primer pools covered more than 80% of
eubacterial sequences in the GreenGenes database with perfectly
matched primer pairs for at least one V-region. In the second design
the amplicons are longer, 300-400 bp products
Our data analysis module classified individual reads by mapping them
to the reference libraries. With the fragment sizes ranging between
200-300 bp, we achieved genus and, in many cases species level
taxonomic resolution, depending on which V-region was evaluated.
In an initial evaluation we tested the complete solution (PCR
chemistry, workflow and software) on two mock community DNA
samples from BEI resources: HM-276D - even community, with equal
number of rDNA copies for each of 20 bacteria and HM-783D–
staggered community, with variable number of rDNA copies. Several
V-regions were amplified by our primer sets for every organism in the
mock community. The number of classified reads in each V-region for
every bacteria depended on both primer complementarity and ease of
sequencing of the particular PCR fragment. Our approach of
interrogating multiple V-regions and sequencing both amplicon strands
improved system robustness against both PCR and sequencing
biases.
The 314v2 chip achieved 1:100 sensitivity (detection of all organisms
in the staggered mock community with 10^4-10^6 rDNA copies/PCR).
Increased sequencing depth (316v2 and 318v2) increased sensitivity
to 1:1000 (10^3-10^6 rDNA copies).
With human samples, we observed no PCR cross-reactivity with
human DNA and were able to identify and determine characteristic Vsignatures
of several important species. The signatures not only help
to increase the confidence in the organism presence and ID, but may
potentially enable strain differentiation.
Survey of multiple V-regions is useful in monitoring changes in the
microbial community compositionIsolation and Identification of MDRO's in the Rio Grande River Poster
Antibiotic resistant bacteria was found in water samples from the Rio Grande River. 19 out of 34 isolated bacterial samples showed resistance to at least 4 classes of antibiotics. Common antibiotic resistant bacteria isolated included E. coli and Klebsiella pneumoniae. The presence of antibiotic resistant bacteria in the river implies that antibiotic resistance is a growing issue affecting an important water source used for agriculture, recreation, and domestic purposes in Texas, Colorado, and New Mexico.
Detection of plant pathogens using non pcr based techniques
This document discusses various molecular techniques for detecting and identifying plant pathogens, beginning with conventional techniques like visual observation, culture-based methods, and microscopy. It then covers several antibody-based techniques like serological methods, ELISA, immunofluorescence, and immunoelectron microscopy. Hybridization methods like Southern blotting, Northern blotting, and DNA microarrays are also introduced. Biochemical approaches involving fatty acid analysis, Biolog identification systems, and volatile compound analysis are briefly covered. The document concludes by discussing the surface plasmon resonance technique for pathogen detection. In summary, it provides an overview of conventional, antibody-based, hybridization-based, and biochemical molecular techniques for plant pathogen detection and identification.
Rapid 16S Next Generation Sequencing for Bacterial Identification in Polymicr...
Rapid 16S Next Generation Sequencing for Bacterial Identification in Polymicr...Thermo Fisher Scientific
In order to identify prokaryotic species in a sample, it is often necessary to culture the sample for hours or days to increase the abundance of bacteria to assayable levels. This often precludes the rapid identification of infectious species.
Furthermore, some species are not easily culturable. We
have developed a facile research method for identifying
bacterial species by 16S ribosomal RNA sequencing on the
Ion Torrent platform. The Ion 16S™ Metagenomics Kit is
designed to PCR amplify the hypervariable regions of the 16S
gene of bacteria. We used this kit to construct libraries from
15 retrospective samples of synovial fluid with various
bacterial species either spiked in or present at collection.
Libraries were sequenced on the Ion PGM™ system and the
data analysis performed using the Ion Reporter™ workflow
which provides an automated analysis solution. Bacteria
present in the samples were correctly identified in samples
containing a single spiked-in species, mixed-species samples,
and in infected samples. Thus, the Ion Torrent™ platform
provides a mechanism for rapidly identifying bacteria that are
present in research samples without culturing.Effective detection of MLN pathogens in leaf tissues and seed lots
The document describes and assesses various detection methods for plant viruses, including Maize Lethal Necrosis virus. It finds that immuno-capture reverse transcription PCR (IC-RT-PCR) combines the specificity of ELISA-based detection with PCR-based detection. A study demonstrated IC-RT-PCR can successfully detect Maize Chlorotic Mottle Virus in infected plant leaves and seeds, with results available in hours and at low labor cost once the technique is established. However, IC-RT-PCR requires specialized equipment and antibodies may not always be available.
cyto2016_emulsion_final
This document summarizes an emulsion sorting technology platform that can be used for high-throughput screening assays in biology. Key applications discussed include:
1) Clonal culturing of microorganisms within emulsion droplets, which allows culturing of microbes that do not form colonies and collection of target droplets.
2) Genetic screening for high functional proteins using emulsion droplets containing both genetic information and expressed proteins, enabling isolation based on protein activity.
3) Digital PCR within emulsion droplets to quantify nucleic acids and selectively recover droplets with fluorescence, applicable to screening cells with specific mutations.
The platform utilizes microfluidic chips to generate and sort monodisperse emulsion droplets, enabling high-throughput analysis and screening that can
Holm_MScThesis
1) The study constructed five cDNA libraries from the vine mealybug, Planococcus ficus, to obtain genetic sequence data for the pest. An RNA extraction protocol was optimized to obtain high quality RNA from the mealybugs.
2) The primary library contained many short inserts, while the fractionated libraries contained size-selected inserts ranging from ~0.25kb to 4kb.
3) A pilot analysis found that 41% of sequences matched databases, mostly being of insect origin. Two potential RNAi targets for mealybug control were identified and seemed unique to arthropods.
Automated system for bacterial identification
[DOWNLOAD IT OPEN IT WITH MICROSOFT POWERPOINT THEN YOU WILL BE ABLE TO UNDERSTAND THE TOPIC COVERED.]
1. WHOLE TEXT IS RELIABLE.
2. TEXT HAS BEEN TAKEN FROM STANDARD TEXT BOOK FOR MEDICAL MICROBIOLOGY.
3. SOME PICTURE HAS BEEN TAKEN FROM JOURNAL.
Sigma Xi 2016
The document discusses developing new shuttle vector technologies for Thermococcus kodakarensis, a hyperthermophilic archaeon. Currently only one shuttle vector exists, limiting genetic techniques. Environmental plasmids from related organisms contain replicative origins and are potential new shuttle vectors, but purifying large amounts has been difficult due to low copy numbers. A transposon-based method is proposed, where the transposon inserts randomly into environmental plasmid DNA. This allows purification in E. coli and assessment of replication in T. kodakarensis, overcoming prior limitations and furthering plasmid biology understanding in archaea.
Journal of Laboratory Automation-2016-Cain-Hom-37-48
This document summarizes the use of acoustic droplet ejection (ADE) liquid handling systems for genotyping genetically engineered mouse models. Key points:
- Traditional liquid handling robots are limited by low throughput, reproducibility issues, and cross-contamination risks. ADE provides contact-free liquid transfer at much higher speeds and precision.
- The authors integrated an ADE system into their workflow for PCR and qPCR reactions, allowing analysis of complex genetic models. ADE increased throughput by 8-10x compared to traditional robots.
- Testing showed ADE greatly improved data reproducibility and consistency for qPCR, while virtually eliminating cross-contamination risks. It also reduced reagent volumes for significant cost savings.
TB presentation
The document provides an overview of tuberculosis (TB) including epidemiology, diagnosis, and laboratory testing. Some key points:
- TB infects millions worldwide each year and is a leading cause of death. Rates are highest in developing countries.
- Diagnosis involves sputum smear microscopy, culture, and molecular testing like PCR. Smear microscopy has low sensitivity but high specificity. Culture is more sensitive but slower.
- Rapid culture methods like BACTEC and MGIT can detect TB in 2-8 days compared to 6-8 weeks for traditional culture.
- Molecular tests like PCR that detect TB DNA sequences like IS6110 can identify TB in smear-negative cases and distinguish TB from
Assessment of microbial population diversity in polymicrobial research sample...
Assessment of microbial population diversity in polymicrobial research sample...Thermo Fisher Scientific
Analysis of 16S sequences in microbial populations using NGS gives a rapid overview of the community diversity, and is usually performed by sequencing one or two hypervariable regions (V-regions), out of the nine present in the 16S rRNA gene. In this study we compared the community structure of fecal, oral and water microbiomes by analyzing sequences from a single variable region, or from the seven V-regions (V2, V3, V4, V6-7, V8 and V9) included into Ion 16S™ Metagenomics Kit (multi-V analysis)DNA-based methods for bioaerosol analysis
Information for producing phylogenetic/taxonomic libraries of airborne bacteria and fungi. Includes fundamental background information, approaches for sequencing and data analysis, two case studies, and a review of sampling methods
16. investigation of infection
Microbiological tests detect microorganisms or the host immune response to infection. They can identify infectious agents, provide information to guide antimicrobial therapy, and assess drug susceptibility. Test results must be interpreted carefully based on factors like specimen type, test characteristics, clinical findings, and communication between clinician and microbiologist. A variety of methods are used, including microscopy, culture, antigen and antibody detection, and nucleic acid amplification tests.
Diagnostic rapide: et si nous copions la nature?
This document summarizes techniques for rapid diagnostic testing by copying nature. It discusses how current culture-based detection of bacteria from clinical samples can take 2-3 days. New molecular detection methods directly detect bacteria in 1-2 hours but sample preparation is the limiting step. The document presents new sample preparation techniques inspired by nature, such as magnetic particle-based extraction of DNA from bacteria and a pelleting method to separate bacteria from blood similar to how horseshoe crabs capture bacteria. Faster sample preparation methods could enable more rapid identification of bacteria using downstream techniques like PCR, sequencing, or mass spectrometry.
Plex ID Congrès SJBM Marseille 2013
Présentation de la technologie Plex-ID par le Pr François Simon lors du Congrès 2013 du Syndicat des Jeunes Biologistes Médicaux (SJBM) à Marseille
6 laboratory diagnosis of bacterial infection
1. Proper specimen collection is essential for accurate laboratory diagnosis of bacterial infections, as the wrong sample, delay in transport, or contamination can limit test usefulness.
2. Common examination methods for diagnosing bacterial infections include morphological analysis, isolation and culture of pathogens, biochemical reactions, antibiotic susceptibility testing, and detection of antigens or nucleic acids.
3. Antibiotic susceptibility testing determines the sensitivity of isolated bacteria to different antibiotics, which helps clinicians select the proper treatment. Methods include minimum inhibitory concentration and disk diffusion tests.
Optical forward-scattering for identification of bacteria within microcolonies
3rd International Conference on Bio-Sensing Technology 2013
This work won the Award for Outstanding Oral Presentation at the 3rd International Conference on Bio-Sensing Technology 2013.
Pierre R. Marcoux, Mathieu Dupoy
Department of Technology for Biology and Healthcare, CEA-LETI MINATEC, 17 avenue des Martyrs, 38054 Grenoble, France.
Antoine Cuer, Joe-Loïc Kodja, Arthur Lefebvre, Florian Licari, Robin Louvet, Anil Narassiguin
These authors contributed equally to this work.
Ecole Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France.
Frédéric Mallard
bioMérieux SA, Innovation & Systems / Technology Research / Sample Prep & Processing Lab, 5 rue des Berges, 38000 Grenoble, France.
The development of methods for the rapid identification of pathogenic bacteria is a major step towards accelerated clinical diagnosis of infectious diseases and efficient food and water safety control. Methods for identification of bacterial colonies on gelified nutrient broth have the potential to bring an attractive solution, combining simple optical instrumentation, no need for sample preparation or labelling, in a non-destructive process. Here, we studied the possibility of discriminating different bacterial species at a very early stage of growth (6 hours of incubation at 37°C), on thin layers of agar media (1mm of Tryptic Soy Agar), using light forward-scattering and learning algorithms (Bayes Network, Continuous Naive Bayes, Sequential Minimal Optimisation). A first database of more than 1000 scatterograms acquired on seven Gram-negative strains yielded a recognition rate of nearly 80%, after only 6 hours of incubation. We investigated also the prospect of identifying different strains from a same species through forward scattering. We discriminated thus four strains of Escherichia coli with a recognition rate reaching 82%. Finally, we show the discrimination of two species of coagulase-negative Staphylococci (S. haemolyticus and S. cohnii), on a commercial selective pre-poured medium used in clinical diagnosis (ChromID MRSA, bioMérieux), without opening lids during the scatterogram acquisition. This shows the potential of this method – non-invasive, preventing cross-contaminations and requiring minimal dish handling – to provide early clinically-relevant information in the context of fully automated microbiology labs.
Cloning_vector_vanshika_varshney
A cloning vector is a genome that can accept the target DNA and increase the number of copies through its own autonomous replication.
An adapter or adaptor, or a linker in genetic engineering is a short, chemically synthesized, single-stranded or double-stranded oligonucleotide that can be ligated to the ends of other DNA or RNA molecules. It may be used to add sticky ends to cDNA allowing it to be ligated into the plasmid much more efficiently.
16s
1) 16S rRNA sequencing is the gold standard for bacterial identification and can identify novel, rare, or aberrant bacterial strains that other phenotypic methods cannot.
2) The document presents data from sequencing 300 clinical isolates, identifying many new species and some new genera, and providing definitive identifications in 88% of cases.
3) While powerful, 16S rRNA sequencing has some limitations like requiring a pure culture and difficulty differentiating closely related species, and interpretation requires consideration of database issues.
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This document discusses molecular diagnostics techniques. It begins by introducing molecular diagnostics and its significance in detecting pathogens, genetic mutations, and biomarkers. It then describes several key techniques used in molecular diagnostics, including nucleic acid amplification methods like PCR, isothermal amplification, and hybridization techniques. It also discusses methods like microarrays, genotyping, and mass spectrometry. The document provides examples of how these techniques are applied to detect various infectious diseases and genetic conditions.
Molecular Environmental Microbiology.ppt
This document discusses molecular microbiology and some of its techniques. It begins by defining molecular microbiology as the study of the molecular basis of physiological processes in microorganisms and manipulation of DNA. It then discusses several molecular techniques used, including polymerase chain reaction (PCR) and its applications such as quantitative real-time PCR and multiplex PCR. The document also discusses uses of molecular microbiology such as detection of pathogens and its role in fields like environmental microbiology.
Applications of Genomic and Proteomic Tools
This document provides an overview of genomic and proteomic tools. It discusses topics like genomics, which is the study of genomes including structural and functional genomics. Proteomics is defined as the large-scale study of proteins, their structures and functions. Several techniques are described briefly, including DNA gel electrophoresis, polymerase chain reaction (PCR), real-time PCR, DNA sequencing, microarray technology, enzyme-linked immunosorbent assay (ELISA), and blotting techniques like Southern blotting, Northern blotting and Western blotting. Applications of these various tools are also mentioned.
Molecular methods of diagnosing infectious disease
Molecular methods such as PCR and LAMP have revolutionized infectious disease diagnosis by allowing rapid and sensitive detection of pathogens. PCR amplifies specific DNA sequences, and real-time PCR with fluorescent probes like TaqMan or molecular beacons allows quantification during amplification. LAMP is an inexpensive isothermal method that amplifies DNA with high sensitivity and specificity using multiple primers and strand displacement. Both PCR and LAMP have advanced diagnosis by detecting pathogens earlier and multiplexing the detection of multiple targets in a single sample.
Micro seminar
Molecular methods such as PCR have revolutionized infectious disease diagnosis by allowing rapid detection of microorganisms. PCR works by amplifying specific DNA sequences using thermal cycling and enzymes. It was developed in the 1980s and has advanced diagnosis by detecting pathogens that were previously difficult to identify. Real-time PCR further improved molecular methods by allowing quantification of amplified DNA sequences in real time through fluorescent reporting. These advances have increased accuracy, precision, and efficiency of diagnostic molecular methods.
cell Viability princes
This document discusses methods for determining cell viability. It defines viability as the capacity for replication over a given timeframe. Methods for counting viable cells include indirect dilution-based techniques where colonies are counted after culturing, and direct techniques like nalidixic acid treatment, fluorogenic dyes, and microradiography that identify viable cells without culturing. A variety of assays can also assess properties of viable cells like integrity, permeability, enzyme content, and energy status to evaluate effects on cell viability.
Advanced diagnostic aids
1. The document discusses various advances in clinical diagnosis, radiographic assessment, microbiological analysis, and characterization of the host response that can aid in the diagnosis of periodontitis.
2. New diagnostic tools discussed include methods to analyze gingival bleeding, temperature, probing depth, digital radiography, subtraction radiography, microbiological assays, and markers in gingival crevicular fluid and saliva.
3. These diagnostic advances provide more sensitive, specific, and quantitative methods for detecting periodontal disease activity and microbial pathogens compared to traditional clinical and radiographic exams.
Advanced Microbiological Diagnostics.pptx
1) Traditional and advanced diagnostic methods are used to support the diagnosis of periodontal diseases, determine disease activity and risk, and monitor periodontal therapy.
2) Common diagnostic aids include bacterial culturing, direct microscopy, immunodiagnostic methods like ELISA and immunofluorescence, and molecular methods like DNA probes, PCR, and pyrosequencing.
3) Advanced methods like PCR and DNA probes are more sensitive than culturing and do not require viable bacteria, though they can have issues with cross-reactivity. Molecular diagnostic tools help facilitate diagnosis, prognosis, risk assessment, and evaluation of treatment response.
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This document discusses waterborne viruses and their detection in water samples. It provides information on different types of viruses found in aquatic systems, including their size and morphology. Smaller viruses are more difficult to remove from water through physical and chemical treatment. The document then discusses the process of collecting and analyzing water samples to detect viruses, including concentrating the viruses, lysing the cells, amplifying the nucleic acids through PCR, and obtaining quantitative results in real-time. Key aspects of primer and probe design for PCR-based detection are also outlined.
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This document summarizes rapid detection methods for foodborne pathogen bacteria. It discusses how foodborne illnesses are a major public health problem and rapid detection of pathogens is needed. Several detection methods are outlined, including traditional culturing as well as newer techniques like PCR, real-time PCR, LAMP, and immunoassays. LAMP is highlighted as a new method that can rapidly detect pathogens under isothermal conditions. The document concludes that LAMP is a promising technique for pathogen detection due to its speed, simplicity and accuracy.
Legionella sampling
The document compares Legionella sampling using culture methods versus PCR testing. While culture has been the gold standard, it is a lengthy process with results taking 12 days. PCR testing provides results much faster within 24 hours and can be automated, though it detects both live and dead cells and issues remain in correlating PCR results to action levels. Guidance is needed on using PCR results to determine appropriate responses to Legionella findings.
LaboratorydiagnosisofTB.pptx
This document provides information on the laboratory diagnosis of tuberculosis. It discusses the classification of mycobacteria, specimen collection, and the various diagnostic methods used which include smear microscopy, culture, and molecular tests. Smear microscopy has limitations but is used in low-resource settings due to its low cost. Culture is the gold standard but is complex and requires biosafety. Liquid culture systems allow for faster results than solid media. Drug sensitivity testing determines resistance and is important for treatment. Molecular tests like line probe assays and GeneXpert can rapidly detect M. tuberculosis and resistance, with GeneXpert suitable for both pulmonary and extrapulmonary samples. Microcare Laboratory in Surat, India provides various tuberculosis diagnostic services and
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This document provides information on the laboratory diagnosis of tuberculosis. It discusses the classification of mycobacteria, specimen collection, and the various diagnostic methods used which include smear microscopy, culture, and molecular tests. Smear microscopy has limitations but is widely used due to its low cost. Culture is the gold standard but is more complex and requires biosafety. Liquid culture systems allow for faster results than solid media. Drug sensitivity testing determines resistance and is important for treatment. Molecular tests like line probe assays and GeneXpert can rapidly detect M. tuberculosis and resistance, with GeneXpert suitable to test pulmonary and some extrapulmonary samples directly. The document concludes with details about Microcare Laboratory which provides accredited tuberculosis diagnostic services
DNA REPLICATION
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- 7. MEASUREMENTS: WHAT IS BEING MEASURED
- 11. RECOVERY RATE FOR LEGIONELLA LABORATORY TESTING METHODS
- 15. SPEED
- 19. DETECTION of VIABLE BUT NON- CULTURABLE BACTERIA
- 22. Lab Culture Test Ithasno methodologyand techniquetodetect legionelladiseasein anon-culturable state.
- 23. CONCLUSION