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
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
evaluation of English Pronunciation and Phonetics for Communication (second edition) and English Phonology (second . textbook is English Phonology written and edited by Wang Wenzhen, which was first published by Shanghai Foreign Language Educational Press in 1999. It was modified and republished in 2008 and also came with a CD. 4 Polyglossia Volume 25, October 2013 2.4 Procedure and Data .