Microbiological aspects in sepsis
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Procalcitonin in sepsis, LDH in sepsis, sample collection for LDH estimation, microbiological aspects of sepsis, ashraf, Lysis centrifugation technique, collection of samples for diagnosis of sepsis, surviving sepsis guidelines, lysis centrifugation technique,
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Antigenic shift and drift
Antigenic shift and antigenic drift are two mechanisms by which influenza viruses evolve. Antigenic shift involves the reassortment of genomic segments between different influenza virus strains, resulting in a virus with a novel combination of surface antigens. This allows the virus to evade existing immunity. Antigenic drift is the accumulation of small mutations in the genes encoding surface antigens, allowing influenza viruses to gradually evade recognition by antibodies. Antigenic drift occurs in both influenza A and B viruses on an annual basis, while antigenic shift is rare but can cause pandemics when it produces a virus with no preexisting immunity in the human population.
Diagnosis of cns infections
Bacterial infections of the central nervous system can cause meningitis, encephalitis, brain abscesses, and CSF shunt infections. Bacterial meningitis is the most common type and occurs when bacteria invade the subarachnoid space and CSF. The incidence is 3-5 per 100,000 people annually in the US. Bacterial meningitis and other CNS infections can cause significant morbidity and mortality if not treated promptly. A lumbar puncture is required to diagnose meningitis by examining the CSF for white blood cell count, differential count, Gram stain, and culture. Proper collection and rapid transport of CSF specimens to the laboratory is critical for accurate diagnosis. [END SUMMARY]
Line probe assay 26 7-15
Line Probe Assay: A New Arrival at the PRL discusses a new diagnostic tool, the line probe assay, that has arrived at the Provincial Tuberculosis Reference Lab in Sindh, Pakistan. The line probe assay can simultaneously detect resistance to rifampicin and isoniazid in mycobacterium tuberculosis, with a sensitivity of over 90% and specificity of over 99% for smear-positive specimens. It provides results faster than conventional drug susceptibility testing methods like solid and liquid culture. The new diagnostic tool will help improve case detection and management of drug-resistant tuberculosis in Pakistan.
SEPSIS BIOMARKERS UPDATES
SEPSIS IS MOST FATAL DISEASE WORLD WIDE. EARLY DETECTION OR PREDICTION OF SEPSIS IS A CHALLENGE
SEPSIS BIOMARKERS ARE OUR WEAPON TO EARLY DETECT SEPSIS. WE HAVE TO UNDERSTAND IT WELL
Fungal diseases intensivist should know
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MTB/RIF Ultra was developed to improve on the sensitivity of the original MTB/RIF assay for detecting tuberculosis (TB), especially in smear-negative and HIV-associated cases. MTB/RIF Ultra uses multiple genetic targets and has a lower limit of detection, resulting in improved sensitivity. It can detect TB at very low bacillary levels and has categories for trace results that may need confirmation with a second specimen. MTB/RIF Ultra performance for rifampicin resistance detection is similar to the original assay. Proper recording of patient category and results is important for correct interpretation. Countries need monitoring plans as they transition cartridge types to track impact.
Influenza
Influenza viruses are RNA viruses in the Orthomyxoviridae family that cause seasonal flu epidemics and pandemics. They are spherical, 80-120nm in size, with segmented negative-sense RNA and replicate in the nucleus. Influenza A has different subtypes based on its hemagglutinin and neuraminidase proteins that determine its antigenicity and ability to cause pandemics through genetic reassortment. Seasonal flu is associated with upper respiratory illness but can lead to pneumonia. Diagnosis involves PCR, antigen detection, virus isolation and serology. Treatment focuses on antivirals while vaccination provides moderate protection against matched strains. High risk groups like the elderly are more susceptible to flu complications.
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Antigenic shift and drift
Antigenic shift and antigenic drift are two mechanisms by which influenza viruses evolve. Antigenic shift involves the reassortment of genomic segments between different influenza virus strains, resulting in a virus with a novel combination of surface antigens. This allows the virus to evade existing immunity. Antigenic drift is the accumulation of small mutations in the genes encoding surface antigens, allowing influenza viruses to gradually evade recognition by antibodies. Antigenic drift occurs in both influenza A and B viruses on an annual basis, while antigenic shift is rare but can cause pandemics when it produces a virus with no preexisting immunity in the human population.
Diagnosis of cns infections
Bacterial infections of the central nervous system can cause meningitis, encephalitis, brain abscesses, and CSF shunt infections. Bacterial meningitis is the most common type and occurs when bacteria invade the subarachnoid space and CSF. The incidence is 3-5 per 100,000 people annually in the US. Bacterial meningitis and other CNS infections can cause significant morbidity and mortality if not treated promptly. A lumbar puncture is required to diagnose meningitis by examining the CSF for white blood cell count, differential count, Gram stain, and culture. Proper collection and rapid transport of CSF specimens to the laboratory is critical for accurate diagnosis. [END SUMMARY]
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Line Probe Assay: A New Arrival at the PRL discusses a new diagnostic tool, the line probe assay, that has arrived at the Provincial Tuberculosis Reference Lab in Sindh, Pakistan. The line probe assay can simultaneously detect resistance to rifampicin and isoniazid in mycobacterium tuberculosis, with a sensitivity of over 90% and specificity of over 99% for smear-positive specimens. It provides results faster than conventional drug susceptibility testing methods like solid and liquid culture. The new diagnostic tool will help improve case detection and management of drug-resistant tuberculosis in Pakistan.
SEPSIS BIOMARKERS UPDATES
SEPSIS IS MOST FATAL DISEASE WORLD WIDE. EARLY DETECTION OR PREDICTION OF SEPSIS IS A CHALLENGE
SEPSIS BIOMARKERS ARE OUR WEAPON TO EARLY DETECT SEPSIS. WE HAVE TO UNDERSTAND IT WELL
Fungal diseases intensivist should know
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MTB/RIF Ultra was developed to improve on the sensitivity of the original MTB/RIF assay for detecting tuberculosis (TB), especially in smear-negative and HIV-associated cases. MTB/RIF Ultra uses multiple genetic targets and has a lower limit of detection, resulting in improved sensitivity. It can detect TB at very low bacillary levels and has categories for trace results that may need confirmation with a second specimen. MTB/RIF Ultra performance for rifampicin resistance detection is similar to the original assay. Proper recording of patient category and results is important for correct interpretation. Countries need monitoring plans as they transition cartridge types to track impact.
Influenza
Influenza viruses are RNA viruses in the Orthomyxoviridae family that cause seasonal flu epidemics and pandemics. They are spherical, 80-120nm in size, with segmented negative-sense RNA and replicate in the nucleus. Influenza A has different subtypes based on its hemagglutinin and neuraminidase proteins that determine its antigenicity and ability to cause pandemics through genetic reassortment. Seasonal flu is associated with upper respiratory illness but can lead to pneumonia. Diagnosis involves PCR, antigen detection, virus isolation and serology. Treatment focuses on antivirals while vaccination provides moderate protection against matched strains. High risk groups like the elderly are more susceptible to flu complications.
New approaches to sepsis - Biomarkers and Molecular Diagnostics (1)
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The document discusses viral hemorrhagic fever (VHF), including:
1. VHF is caused by several viruses from four virus families and is characterized by fever and hemorrhaging.
2. Transmission occurs from animal reservoirs to humans and between humans. Incubation periods vary from 4-21 days depending on the virus.
3. Diagnosis involves hematological, coagulation, and biochemical testing as well as virus detection methods like RT-PCR, ELISA, and virus isolation.
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Rabies
Rabies is a fatal viral disease transmitted through the saliva of infected animals, most commonly dogs. It causes encephalitis and is nearly 100% fatal once symptoms develop. India accounts for over 20,000 deaths from rabies annually, mostly rural children. The rabies virus infects the central nervous system and causes symptoms like hydrophobia, aerophobia and aggression. It is important to properly manage animal bites to prevent transmission, through timely vaccination and immunoglobulin administration depending on the category of bite. While there is no cure once symptoms develop, rabies can be effectively prevented through proper animal bite management.
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This document summarizes laboratory diagnosis methods for respiratory tract infections. It describes tests to identify streptococcus pyogenes from throat samples to diagnose pharyngitis, and Epstein-Barr virus antibodies or Monospot tests to detect infectious mononucleosis. For pneumonia, it outlines identifying streptococcus pneumoniae or klebsiella pneumoniae from sputum through gram staining and culture. Finally, it discusses detecting Mycobacterium tuberculosis from sputum through acid-fast staining, culturing, or PCR to diagnose tuberculosis.
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This document discusses conventional laboratory methods for diagnosing tuberculosis (TB), including specimen collection, processing, and microscopy techniques. Key points:
- Sputum and other respiratory samples are most commonly collected and must be handled safely due to the infectious nature of TB.
- Samples undergo decontamination to reduce contamination using agents like N-acetyl-L-cysteine plus sodium hydroxide before centrifugation to concentrate the bacteria.
- Microscopy techniques like Ziehl-Neelsen staining are used for presumptive identification by examining acid-fast bacilli in stained smears, though sensitivity is low. Culture remains the gold standard for definitive diagnosis.
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This document provides guidance on antibiograms, which are profiles of antimicrobial susceptibility testing results that summarize percentages of microorganisms susceptible to various drugs. It discusses generating antibiograms from aggregate laboratory data and including only clinically useful drugs. Methods for measuring susceptibility like disc diffusion and broth dilution are outlined. Recommendations include analyzing data annually and only including common species and diagnostic isolates. Antibiograms help guide empirical treatment and detect resistance trends. Limitations include potential biases and small isolate numbers reducing significance.
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Phenotypic methods used in antimicrobial susceptibility testing
This document provides instructions for performing antimicrobial susceptibility testing using phenotypic disk diffusion methods according to EUCAST guidelines. It describes the appropriate media, inoculum preparation, application of antimicrobial disks, incubation conditions, and reading of zone diameters. Mueller-Hinton agar is used for non-fastidious bacteria, while Mueller-Hinton with 5% blood and β-NAD is used for fastidious organisms. The inoculum is adjusted to a 0.5 McFarland standard and disks are applied and incubated according to organism-specific timeframes and conditions. Zones are read at the point of complete inhibition while accounting for any colonies within zones or fuzzy edges.
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Specimen collection for clinical microbiology laboratory
The document discusses guidelines for proper specimen collection for clinical microbiology laboratories. It emphasizes that specimen quality is critical for accurate laboratory diagnosis and interpretation. Specimens should be collected aseptically according to standardized procedures and transported promptly to the laboratory. Specific collection details are provided for various specimen types, including blood, urine, sputum and tissues. Adherence to these specimen collection protocols helps ensure microbiology testing provides meaningful and reliable results.
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The document discusses viral hemorrhagic fever (VHF), including:
1. VHF is caused by several viruses from four virus families and is characterized by fever and hemorrhaging.
2. Transmission occurs from animal reservoirs to humans and between humans. Incubation periods vary from 4-21 days depending on the virus.
3. Diagnosis involves hematological, coagulation, and biochemical testing as well as virus detection methods like RT-PCR, ELISA, and virus isolation.
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Diagnosis of pneumonia can be challeging, especially if pathogens other than Streptococcus pneumoniae are involved Multiplex PCR with results available within the same day can investigate the presence or absence of 16 viruses and 5 bacteria, enablng the physician to make informed decisions about treatment, prognosis and public health and infection control measures.
Antibiogram
This document provides an antibiogram for Jindal Institute of Medical Science summarizing the types of bacterial isolates found from patient samples over a one month period and their antibiotic sensitivities. It lists the most common gram positive and gram negative isolates from urine, sputum/endotracheal secretions, pus, and blood samples. It then details the sensitivity of these isolates to various antibiotics, with E.coli and Klebsiella being highly sensitive to imipenem, amikacin and piperacillin-tazobactam according to the data. The document concludes with rates of multidrug-resistant organisms identified.
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Dengue
Dengue is a rapidly spreading mosquito-borne viral disease that infects an estimated 50 million people annually. Laboratory diagnosis of dengue is important for early detection, confirmation of clinical diagnosis, surveillance, outbreak control, and research. During the acute phase within 5 days of illness, the virus can be detected through virus isolation, nucleic acid detection, or antigen detection (NS1). After the acute phase, antibodies are detected - IgM appears first and indicates a primary infection, while IgG indicates a secondary infection. IgM levels peak at 2 weeks and decline over 2-3 months. IgG levels rise more slowly but persist for months or life. The IgM/IgG ratio can distinguish primary from secondary infection. Patient monitoring
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This document provides information about Bordetella pertussis and whooping cough. It discusses how B. pertussis was identified in 1900 by Jules Bordet and Gengou as the bacteria that causes whooping cough. It describes the symptoms and stages of whooping cough including the catarrhal, paroxysmal, and convalescent stages. It also discusses how whooping cough can be diagnosed through culture, PCR, or serological testing and treated through vaccination with the DTaP vaccine.
Rabies
Rabies is a fatal viral disease transmitted through the saliva of infected animals, most commonly dogs. It causes encephalitis and is nearly 100% fatal once symptoms develop. India accounts for over 20,000 deaths from rabies annually, mostly rural children. The rabies virus infects the central nervous system and causes symptoms like hydrophobia, aerophobia and aggression. It is important to properly manage animal bites to prevent transmission, through timely vaccination and immunoglobulin administration depending on the category of bite. While there is no cure once symptoms develop, rabies can be effectively prevented through proper animal bite management.
Sepsis markers
This document discusses sepsis markers that can be used for the diagnosis, assessment, and prognosis of sepsis. It describes several commonly used markers including lactate, C-reactive protein (CRP), and procalcitonin (PCT). Lactate levels indicate tissue hypoperfusion and are prognostic, with higher lactate clearance associated with lower mortality. CRP is an acute phase protein that rises within hours of infection but can remain elevated. PCT rises more quickly than CRP and correlates better with sepsis severity and outcome. Newer markers like presepsin and heparin-binding protein show promise as early markers of sepsis. No single marker is perfect and combinations may provide better diagnosis and guidance of sepsis management and
Medical Microbiology Laboratory (Chlamydia spp.)
This document provides information about Chlamydia species, including their taxonomy, life cycle, diseases they cause, and methods for laboratory diagnosis. It describes Chlamydia as obligate intracellular parasites that infect humans, animals, and birds. They have both a replicative, reticulate body form and an infective, elementary body form. Key diagnostic methods discussed are microscopy using stains like Giemsa to identify inclusion bodies, culture isolation, antigen detection by ELISA or PCR, and antibody detection by tests like complement fixation. Treatment involves antibiotics like tetracyclines or azithromycin.
Microbiology (laboratory diagnosis of respiratory tract infections)
This document summarizes laboratory diagnosis methods for respiratory tract infections. It describes tests to identify streptococcus pyogenes from throat samples to diagnose pharyngitis, and Epstein-Barr virus antibodies or Monospot tests to detect infectious mononucleosis. For pneumonia, it outlines identifying streptococcus pneumoniae or klebsiella pneumoniae from sputum through gram staining and culture. Finally, it discusses detecting Mycobacterium tuberculosis from sputum through acid-fast staining, culturing, or PCR to diagnose tuberculosis.
Covid 19 sample collection and diagnosis
This document provides information on collecting, processing, and diagnosing COVID-19 samples through various methods. It discusses proper sample collection and labeling, as well as packaging and transportation guidelines. The main diagnostic tests described are RT-PCR, which is the gold standard; TRUENAT and CBNAAT, which are chip-based and cartridge-based PCR machines; point-of-care rapid antigen tests; and antibody tests. Precautions for handling specimens and limitations of each test are also outlined.
Conventional lab diagnosis of tb
This document discusses conventional laboratory methods for diagnosing tuberculosis (TB), including specimen collection, processing, and microscopy techniques. Key points:
- Sputum and other respiratory samples are most commonly collected and must be handled safely due to the infectious nature of TB.
- Samples undergo decontamination to reduce contamination using agents like N-acetyl-L-cysteine plus sodium hydroxide before centrifugation to concentrate the bacteria.
- Microscopy techniques like Ziehl-Neelsen staining are used for presumptive identification by examining acid-fast bacilli in stained smears, though sensitivity is low. Culture remains the gold standard for definitive diagnosis.
Antibiogram CLSI Recommendations
This document provides guidance on antibiograms, which are profiles of antimicrobial susceptibility testing results that summarize percentages of microorganisms susceptible to various drugs. It discusses generating antibiograms from aggregate laboratory data and including only clinically useful drugs. Methods for measuring susceptibility like disc diffusion and broth dilution are outlined. Recommendations include analyzing data annually and only including common species and diagnostic isolates. Antibiograms help guide empirical treatment and detect resistance trends. Limitations include potential biases and small isolate numbers reducing significance.
Acinetobacter
Acinetobacter is a genus of gram-negative bacteria that includes opportunistic pathogens. The most clinically important species are A. baumannii and A. lwoffii. A. baumannii is commonly found in hospitals and can cause infections in immunocompromised patients. It is able to survive on surfaces and in the environment. Treatment is challenging due to high levels of antibiotic resistance, though carbapenems and polymyxins may be used. Proper hygiene and cleaning can reduce transmission in clinical settings.
Phenotypic methods used in antimicrobial susceptibility testing
This document provides instructions for performing antimicrobial susceptibility testing using phenotypic disk diffusion methods according to EUCAST guidelines. It describes the appropriate media, inoculum preparation, application of antimicrobial disks, incubation conditions, and reading of zone diameters. Mueller-Hinton agar is used for non-fastidious bacteria, while Mueller-Hinton with 5% blood and β-NAD is used for fastidious organisms. The inoculum is adjusted to a 0.5 McFarland standard and disks are applied and incubated according to organism-specific timeframes and conditions. Zones are read at the point of complete inhibition while accounting for any colonies within zones or fuzzy edges.
Biomarkers in sepsis
This document discusses the potential utility of biomarkers for diagnosing and prognosing sepsis. It begins by explaining why improving diagnostic and prognostic tools for sepsis is important, as it is a leading cause of death in ICU patients. It then discusses how early detection and treatment are paramount but current detection strategies are limited. The document introduces the biomarker paradigm for sepsis, where biomarkers can identify inflammation, coagulation, tissue damage and repair processes to better stratify severity and prognosticate outcomes. Several candidate biomarkers are discussed, such as procalcitonin, cytokines, chemokines, and pentraxin 3. The document considers how biomarkers may help with diagnosis, prognostication, and identifying high-risk patients and treatment response. It concludes the future
MRSA Detection
This document discusses methods for detecting Methicillin-Resistant Staphylococcus aureus (MRSA). MRSA is any strain of S. aureus that is resistant to beta-lactam antibiotics due to the mecA gene. Rapid detection of MRSA is important for optimal treatment and reducing costs. The document describes several screening methods, focusing on the oxacillin salt agar screening test which involves growing bacterial samples on agar containing oxacillin and 4% NaCl. Growth of more than one colony indicates oxacillin resistance and identifies the strain as MRSA.
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Microbiology lec4
1) The document discusses various species of streptococci bacteria including Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus pneumoniae, Enterococci, and Viridans streptococci.
2) S. pyogenes is known to cause infections like strep throat, scarlet fever, and toxic shock syndrome. It is identified by beta hemolysis on blood agar and sensitivity to bacitracin. Complications can include rheumatic fever and glomerulonephritis.
3) S. agalactiae commonly causes neonatal infections like sepsis and meningitis. It is identified through CAMP testing and hippurate hydrolysis.
6 Neonatal Septicemia
Neonatal sepsis is a serious infection that can affect newborns, especially those born prematurely or with low birth weight. The immaturity of a newborn's immune system makes them highly susceptible to infection. Symptoms of neonatal sepsis are non-specific and can include poor feeding, temperature instability, and respiratory distress. Diagnosis relies on clinical signs and abnormal laboratory test results, as there is no single diagnostic marker. Treatment involves administering broad-spectrum antibiotics early while infection is considered, with supportive care and management of any complications.
Neonatal sepsis
Neonatal sepsis is defined as a clinical syndrome of infection occurring in the first month of life, characterized by non-specific signs and symptoms. It can involve septicemia, pneumonia, or meningitis. Common causative organisms include E. coli, Staphylococcus aureus, Group B Streptococcus, and Klebsiella species. Risk factors include prematurity, prolonged rupture of membranes, and maternal fever. Diagnosis involves a sepsis screen of a complete blood count, blood culture, and C-reactive protein level. Treatment involves broad-spectrum antibiotics like ampicillin and gentamicin or cefotaxim and amikacin with supportive care. Outcomes depend on gestational age,
Neonatal Sepsis And Recent Challenges
Neonatal sepsis remains a challenge, with rates varying significantly between institutions. While early-onset sepsis is usually caused by bacteria acquired before or during birth, late-onset sepsis often results from bacteria acquired after birth in the NICU. Diagnosis relies on clinical signs and laboratory tests like blood cultures and CRP levels. New diagnostic methods including PCR and microarrays show promise, but further studies are needed. Treatment requires appropriate empiric antibiotics while cultures are pending, with adjustments based on identified organisms and developing antimicrobial resistance patterns.
Sepsis
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Analysis of Body Cavity Fluids
Sep 08, 2014
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Analysis of Body Cavity Fluids. Lab 8. Indications and Sampling. Indications: - Identifies the type of fluid present: transudate, exudate, neoplastic or other effusion and may identify the cause of fluid accumulation Sampling: - Sterile preparation of site
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Analysis of Body Cavity Fluids
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Analysis of Body Cavity Fluids Lab 8
Indications and Sampling Indications: - Identifies the type of fluid present: transudate, exudate, neoplastic or other effusion and may identify the cause of fluid accumulation Sampling: - Sterile preparation of site - Use a fine needle (21- 23 G) - Avoid movement or causing pain during sampling - Split sample into EDTA & plain sterile tubes - Process as soon as possible - Monitor the animal
Tests Applied Four basic tests are applied: • Appearance of fluid • Protein content • Nucleated cell count (NCC) • Examination of a direct and/or sediment smear to identify cell type Additional tests such as biochemistry may be used in certain clinical situations, e.g. urea or creatinine, if uroabdomen (from bladder rupture) is suspected.
Specimen Management for Smears - Mix sample well - Make a direct smear - Centrifuge & smear the deposit (sediment smears) - Air-dry rapidly & stain Special centrifuges (cytocentrifuges) yield better smears A standard centrifuge may be used at a slow speed for a short period (<1000 rpm)
Procedure to get a smear “Wedge” method Flat-slide method A drop of the fluid is placed on a cleaned glass slide A smear can be made by the “wedge” method used for making blood smears Alternatively, a 2nd slide may be superimposed on the first, and the two are drawn smoothly apart to make two thin smears.
Examination of sediment smears • Blood stains e.g. Diff-Quik or Giemsa usually used • The smear is scanned at low power, to locate cells and cell clusters • NORMAL FINDINGS: N
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- 16. DETECTION OF BACTEREMIA AND FUNGEMIA • Samples directly taken from patients • PCR- simultaneous detection of organism along with resistant genes (oxacillin, vanco, carbapenems) • Results – few hours • Not cost effective 16Md Ashraf Ali
- 17. Summary Test Sample Volume Container Blood culture Whole blood 10ml Nutrient medium Lactate assay Plasma 1 ml Sodium Fluoride (gray tube) Procalcitonin Serum 0.5ml Sterile vaccutainer C-reactive protein Serum 0.5ml Sterile vaccutainer 17Md Ashraf Ali
- 18. Md Ashraf Ali 18
Editor's Notes
- No role for lactate in diagnosis of early sepsis
- Offsite Collection: It is recommended to draw lactic acid without a tourniquet or immediately after applying the tourniquet. If the tourniquet is applied for an extended time, remove the tourniquet and let the blood circulate two minutes prior to retrying the draw. Collect specimen in gray top tube. Invert tube gently to mix. Place specimen on ice. Centrifuge, aliquot plasma into a plastic vial within 15 minutes of collection and freeze immediately. Test Methodology: Colorimetric Enzyme Assay
- Two-step enzyme immunoassay sandwich method with fluorescent detection