An Introduction To Clinical Microbiology - Mount Sinai Hospital

2y ago
65 Views
5 Downloads
3.62 MB
98 Pages
Last View : 6d ago
Last Download : 5m ago
Upload by : Ronan Orellana
Transcription

TO Public Health January 17, 2007An Introduction toClinical MicrobiologySusan M. Poutanen, MD, MPH, FRCPCMicrobiologist & Infectious Disease ConsultantDepartment of Microbiology

Objectives1. To provide an introduction to a typicalmicrobiology laboratory2. To address specific microbiologylaboratory test issues as they apply topublic healthDepartment of Microbiology

Who we are Shared microbiology service between TML(UHN & MDS) and MSH Serve nine Ontario hospitals ( 5000 beds)and five non-hospital clients Approximately 35 000 specimensprocessed per monthDepartment of Microbiology

Who we are Site:– 14th Floor Mount Sinai Hospital Website:– www.microbiology.mtsinai.on.caDepartment of Microbiology

What we do Clinical Service– Routine Diagnostics– Infection Control– Reference Testing Research EducationDepartment of Microbiology

What we do Clinical Service– Routine Diagnostics– Infection Control– Reference Testing Research EducationDepartment of Microbiology

Clinical ServiceDepartment of Microbiology

A. Routine Diagnostics cobacteriologyDepartment of Microbiology

Terminology Bacteriology– Prokaryotic, single cell organisms– Divided into aerobic and anaerobic– Divided into gram-positive and gram-negative Mycology– Eukaryotic, multi-cellular organisms– Divided into yeast and filamentous fungiDepartment of Microbiology

Terminology Virology– Acellular infectious particles consisting of coreof RNA or DNA surrounded by a protein coatunable to replicate without a host cell Serology– Detection of antibodies against infectiousagentsDepartment of Microbiology

Terminology Parasitology– Eukaryotic organisms– Divided into protozoa (e.g. Plasmodium spp.,Giardia lamblia) and nematodes (i.e. worms) Mycobacteriology– Prokaryotic, single cell organisms– Acid-fast bacteriaDepartment of Microbiology

Process Specimen collectionSpecimen receiptSpecimen processingTestingInterpretationReportingDepartment of Microbiology

Specimen Collection Receipt Transport media– Stool cultures (Cary-Blair)– Viral/Mycoplasma/Chlamydia (transport media) Transport temperature– Sterile Site Specimens (room temp/incubate)– Nonsterile Site Specimens (room temp/4oC)– Virology/Serology/NAAT (4oC)Department of Microbiology

Tests Overview Direct detection– Stained smears, EM, LA, DFA, EIA, NAAT Culture– Media, Cell lines Serology– EIA, IFA, Immunoblots Susceptibility TestingDepartment of Microbiology

Direct DetectionDepartment of Microbiology

The Gram StainDepartment of Microbiology

Department of Microbiology

Bacterial ClassificationGram StainGram PositiveCocciAnaerobice.g. peptostreptococcusGram NegativeBacilliAerobicClustere.g. StaphylococcusAnaerobice.g. Clostridia, ActinomycesChainse.g. StreptococcusCoccie.g. Haemophilus, Moraxella, NeisseriaAerobice.g. Listeria, CorynebacteriumBacilliAerobicLactose Fermentere.g. Klebsiella, E coliEnterobacterAnaerobice.g. BacteroidesNon-lactose fermenterOxidase Positivee.g. PseudomonasOxidase Negativee.g. Serratia, Proteus,Acinetobacter,SternotrophomonasDepartment of Microbiology

Calcofluor WhiteDepartment of Microbiology

Electron MicroscopyNorovirus by EMDepartment of Microbiology

Latex Agglutination Cryptococcal Antigen(CRAG)Department of Microbiology

DFA/IFADepartment of Microbiology

Membrane EIAsDepartment of Microbiology

NAAT PCR most common Real-time instrumentsDepartment of Microbiology

PCRDepartment of Microbiology

Culture – MediaDepartment of Microbiology

Department of Microbiology

Department of Microbiology

Department of Microbiology

Department of Microbiology

THERMONUCLEASE TESTDepartment of Microbiology

Department of Microbiology

Department of Microbiology

Department of Microbiology

Department of Microbiology

Department of Microbiology

Department of Microbiology

Department of Microbiology

Department of Microbiology

Automated IdentificationDepartment of Microbiology

Culture – Cell LinesDepartment of Microbiology

Tube CultureDepartment of Microbiology

Vero Cells – SARS-CoVDepartment of Microbiology

Shell VialDepartment of Microbiology

SerologyDepartment of Microbiology

Serologic Tests Enzyme Immunoassay (EIA)Immunofluorescent Assays (IFA)Complement Fixation (CF)Hemagglutination Inhibition Assays (HAI)Western BlotNeutralization TestsDepartment of Microbiology

EIADepartment of Microbiology

IFADepartment of Microbiology

CFDepartment of Microbiology

W. BlotDepartment of Microbiology

HAIDepartment of Microbiology

Neutralization Tests Neutralization of a virus is defined as theloss of infectivity through reaction of thevirus with specific antibody Virus and serum are mixed underappropriate condition and then inoculatedinto cell culture, eggs or animalsDepartment of Microbiology

Titres Dilute specimen to determine howconcentrated antibody titre is Expressed as 1:8, 1:16, 1:32, 1:64 etc. Positive– IgM test– set cutoff (specific to each agent)– 4 fold rise between acute and convalescentspecimensDepartment of Microbiology

Susceptibility TestingDepartment of Microbiology

Definitions MIC (Minimum Inhibitory Concentration) MBC (Minimum Bactericidal Concentration) Tolerance– MBC/MIC 32– Clinical relevance not established– Mostly related to beta-lactam drugsDepartment of Microbiology

DefinitionsCombination Testing MCBT (multiple combination bactericidaltesting) Synergy Testing (synergy, indifference,antagonism)– Checkerboard Titration– Time Kill CurvesDepartment of Microbiology

MIC Interpretive Standards– NCCLS (changed to CLSI in Jan 2005)– Susceptible (S), Intermediate (I), Resistant (R) MIC breakpoints based on studies assessing:– PK/PD based on systemic antibiotic delivery– Clinical efficacy studies» Clinical resistance vs. biologic resistanceDepartment of Microbiology

Department of Microbiology

Susceptibility Testing Bacterial––––––Agar dilution, broth macrodilution, broth microdilutionAutomated broth microdilutionDisk diffusionE testScreening PlatesMolecular (latex agglutination, NAAT) Fungal– Macrodilution, microdilution Mycobacteriology– MacrodilutionDepartment of Microbiology

Susceptibility Testing Bacterial––––––Agar dilution, broth macrodilution, broth microdilutionAutomated broth microdilutionDisk diffusionE testScreening PlatesMolecular (latex agglutination, NAAT) Fungal– Macrodilution, microdilution Mycobacteriology– MacrodilutionDepartment of Microbiology

Agar DilutionPenicillin1 mg/LPenicillin2 mg/LPenicillin4 mg/LDepartment of Microbiology

Agar DilutionPenicillin1 mg/LPenicillin2 mg/LPenicillin4 mg/LDepartment of Microbiology

Agar DilutionPenicillin1 mg/LPenicillin2 mg/LPen MIC 4 mg/LPenicillin4 mg/LDepartment of Microbiology

Broth Macrodilution Testing1248 16 32 64 128 256 512Penicillin (mg/L)Department of Microbiology

Broth Macrodilution Testing1248 16 32 64 128 256 512Penicillin (mg/L)Department of Microbiology

Broth Microdilution TestingDepartment of Microbiology

Broth Microdilution TestingDepartment of Microbiology

Broth Microdilution TestingDepartment of Microbiology

Broth Microdilution TestingDepartment of Microbiology

Broth Microdilution TestingMupirocin (mg/L)1 2 4 8 16 32 64 128 256Mupirocin MIC 128 mg/LDepartment of Microbiology

Automated Broth MicrodilutionDepartment of Microbiology

Disk Diffusion TestingDepartment of Microbiology

Disk Diffusion TestingDepartment of Microbiology

Disk Diffusion TestingDepartment of Microbiology

E testDepartment of Microbiology

E testDepartment of Microbiology

Screening Plates(DIRECT FROM ISOLATE)Department of Microbiology

Screening Plates(DIRECT FROM SPECIMEN)Department of Microbiology

Latex AgglutinationDepartment of Microbiology

NAATDepartment of Microbiology

Limitations of Susceptibility Tests Interpretative guidelines Cost (NAAT) New resistance determinants– MRSA– VRE– ESBL– VRSA, VISA Turn-around-timesDepartment of Microbiology

Turn-around-times (TATs)Department of Microbiology

TATs Direct detection– STAT or within 24 hours Culture– Varies Serology– Usually within 24 hours (excluding weekends) Susceptibility Testing– Varies (typically requires positive culture)Department of Microbiology

Culture TATs Bacteriology– Routine: 24-48 hours– BC: 5 days (21 days if endocarditis) Mycology– 2-6 weeks Virology– 1-2 weeks Mycobacteriology– 6 weeksDepartment of Microbiology

B. Infection Control Epidemiology of Infectious Disease– Reportable diseases– Tracking rates of select pathogens e.g. C. difficile, AROs Epidemiology of Antimicrobial Resistance– Annual antibiogram– Antibiotic Subcommittee Formulary, guidelines Outbreak investigation– Epidemiology typing, treatment optionsDepartment of Microbiology

PFGEDepartment of Microbiology

eg.S123MS456Skb- 593- 447- 364- 304-184-105Department of Microbiology

C. Reference Work Susceptibility testingIdentifying resistance determinantsEpidemiologic typing (esp. AROs)NAATDepartment of Microbiology

ResearchDepartment of Microbiology

Research Collaborative studiesSurveillance studiesMechanisms of resistanceAnimal model– PK/PD– MPCDepartment of Microbiology

EducationDepartment of Microbiology

Education Undergraduate lectures Postgraduate lectures Plate rounds– ID team with pharmacists Internships– Students– Pharmaceutical industry representativesDepartment of Microbiology

ResourcesDepartment of Microbiology

labs/specimen.htmlDepartment of Microbiology

labs/specimen.htmlDepartment of Microbiology

Department of Microbiology

OPHL “For further assistance, please use theOPHL HELPLINE at 1-800-640-7221 andyour call will be appropriately directed.”Department of Microbiology

Susan M. Poutanen, MD, MPH, FRCPCspoutanen@mtsinai.on.ca(416) 586-3139Department of Microbiology

An Introduction to Clinical Microbiology Susan M. Poutanen, MD, MPH, FRCPC . Objectives 1. To provide an introduction to a typical microbiology laboratory 2. To address specific microbiology laboratory test issues as they apply to public health. Department of Microbiology Who we are Shared microbiology service between TML (UHN & MDS) and MSH

Related Documents:

What is Clinical Microbiology? Function of the clinical microbiology laboratory: Clinical: diagnosis and management of infections Epidemiological: understand infectious microbes in patients and populations, and to find sources and routes of transmission necessary for prevention efforts General rules in clinical microbiology: #1:

Clinical Microbiology Kuwait Board Curriculum & General Objectives 2014 The educational program provides: 1. A broad understanding of the diagnosis and management of infectious disease from a clinical and laboratory perspective 2. The diagnostic techniques required in the practice of clinical microbiology 3. understanding of the areas of clinical microbiology detailed in the curriculum 4 .

Industrial microbiology Medical and pharmaceutical microbiology Rumen microbiology Space microbiology 1.2 Definitions Milk and milk products occupy a more significant role in the human food profiles. The study of microorganisms that are associated with milk and milk products in all aspects is defined as "Dairy Microbiology". 1.2 .

Title: Clinical Microbiology Users Handbook QP Ref: LH-MIC-GEN-G-001v1 Author: Jennifer Challoner & Alex Duggan Authorised by: Microbiology Specialty board Created Date:23rd April 2020 Disposal date: 22nd April 2050 Page 1 of 75 9693 Microbiology Laboratory Handbook Microbiology Laboratory North Tyneside General Hospital Rake Lane North Shields Tyne & Wear NE29 8NH This SOP supersedes all .

General Microbiology Manual _ Abdelraouf A. Elmanama Ph. D Microbiology 7 Introduction Welcome to the microbiology laboratory. The goal of the laboratory is to expose students to the wide variety of lives in the microbial world. Although the study of microbiology includes

Microbiology H Core 4 3 30 70 100 4 MBH- 204 Food Microbiology H Core 4 3 30 70 100 4 MBS- 205 Bioinformatics S Core 2 2 15 35 50 2 Practical MBP- 206 Microbial Genetics, Molecular Biology Pract 4 4 30 70 100 4 MBP- 207 Environmental Microbiology and Food Microbiology Pract 4 4 30 70 100 4

Microbiology Categories. Microbiology . Microbiology Categories Standard . Guidance; Microbiology Standard of Practice 1 (MB S1): Biological . Additional required use of the BSC should be established by the laboratory director

It would be called the American Board of Radiology. A short time after his speech to the ACR, Dr. Christie repeated his proposal at a session of the American Medical Association (AMA) Section on Radiology in June 1933. It was received favorably. After two years of discussion among representatives of the four major national radiology societies (ACR, ARRS, ARS, and RSNA), the ABR was .