Microbiology laboratories: some relevant definitions and elements of biosafety

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Microbiology laboratories: some relevant definitions and elements of biosafety

Transcript of Microbiology laboratories: some relevant definitions and elements of biosafety

Page 1: Microbiology laboratories: some relevant definitions and elements of biosafety

Microbiology laboratories: some relevant definitions and

elements of biosafety

Page 2: Microbiology laboratories: some relevant definitions and elements of biosafety

Relevant definitions

Pathogens

• microorganisms or infectious agents (bacteria, fungi, viruses, rickettsiae, chlamydiae, mycoplasmas, parasites and prions) capable of causing disease in humans, animals or plants

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Relevant definitions

Infection• Invasion by and multiplication of a microorganism or

infectious agent in a bodily part or tissue ± tissue injury and progress to disease

Colonisation

• first stage of infection; pathogen situated at possible appropriate entry site (urogenital, digestive, respiratory, conjunctiva) – not necessarily followed by infection

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Relevant definitions - continued

Infectivity

• Capacity of pathogen to enter, survive and multiply in a susceptible host

Pathogenicity • Capacity of pathogen to produce disease in a susceptible

host

Susceptible host

• Organism (human, animal) which can be infected by pathogen (defense mechanisms are defeated by pathogen)

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The infectious process

Relationship between PATHOGEN and HOST

• Dynamic: reciprocal influences• Specific:

– host & tissue specificity (certain pathogens selectively infect certain tissues/cells)

• Depends on:

– Virulence of pathogen vs. Susceptibility / Resistance of host

– Exposure (pathogen meets susceptible i.e. suitable host)

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The infectious process - continued

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New HOSTSusceptible?Age, Gender,

Genetics, Immunity, Prevention

EXITBody fluids /Containment

breach

RESERVOIRInfected host /

Lab sample

ENTRYRespiratory,Digestive,

Skin, Membranes

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Some factors which influence the occurrence of infection

Pathogen related:•Survival time of pathogen outside (suitable) host•Infective dose (quantity of pathogen required to produce infection)•Transmission routes (inhalation, ingestion, percutaneous, sexual, etc)

Host related:•Susceptibility (age, immune status)•Preventive means (vaccination, others)

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Survival outside host (after Walther B.A., Ewald P.W., 2004)

Variola virus • years - patient exudate, room temperature, dark

• ~ 80 days – vesicle fluid, room temperature, dark

Mycobacterium tuberculosis

• 90 – 300 days – sputum, room temperature, dark• 10 – 120 days – dust (floor/objects/fabric), room

temperature

Neisseria meningitidis

• 1 day – glass/plastic/fabric, suspension, room T°, dark˂Hepatitis B Virus

• - at least 7 days

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Survival outside host (continued)

Spores: reproductive structures adapted

for longtime survival in unfavourable

conditions

(etymology: ancient Greek spora = seed)

Bacterial spores - outer layer of keratin resistant to chemicals, staining and heat → bacterium able to stay dormant for years, protected from temperature differences, absence of air, water and nutrients

Spore forming bacteria: • Clostridium spp (e.g. Clostridium difficile, Clostridium tetani); • Bacillus spp (B. anthracis).

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Relevant definitions - continuedPathogen Minimal infective dose

S. pyogenes, S. aureus Under 103 CFU

Shigella (virulent strains) As low as 10 CFU

Bacillus anthracis 104 spores !!

Brucella species 10-100 organisms

Francisella tularensis 10-50 organisms

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EBSA pre-conference course, Basel, 18 June 2013

Classification of microorganisms Risk groups (1-4)

Risk group 1 (no / low individual & community risk)

• human / animal disease – unlikely

e.g. E.coli non-pathogenic strains, Lactobacillus spp.

Risk group 2 (moderate individual & low community risk)• ability to cause human / animal disease

• laboratory exposure → possible infection (severe)• availability of prevention & treatment

e.g. Corynebacterium diphtheriae, Haemophilus influenzae, E.coli, Orthomyxoviridae (Influenza viruses)

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EBSA pre-conference course, Basel, 18 June 2013

Risk groups (1-4) (continued)

Risk group 3 (high individual & low community risk)

• serious human / animal disease• respiratory transmission (aerosolization)• no interpersonal respiratory transmission (usually) +

exceptions!*• availability of prevention & treatment

e.g. E.coli O157:H7, Francisella tularensis type A, Flaviviridae (West Nile Virus), Hepadnaviridae (HBV),

+ M. tuberculosis* (interpersonal respiratory transmission present)

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EBSA pre-conference course, Basel, 18 June 2013

Risk groups (1-4) (continued)

Risk group 4 (high individual & high community risk)

• serious human & animal disease• respiratory transmission

• interpersonal transmission possible• NO prevention & treatment

e.g. Filoviridae (Ebola, Marburg), Arenaviridae (Lassa)

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EBSA pre-conference course, Basel, 18 June 2013

Why risk groups?

• Requirements for sample processing

Premises (location, construction)Equipments

MaterialsStaff related requirements (number, qualifications, training)

Procedures

Biosafety Levels (BSL)

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EBSA pre-conference course, Basel, 18 June 2013

Biosafety Level I (BSL I)Agents Not known to cause diseases in healthy adults

Practices Standard microbiological practices

Primary barriers

None

PPE Laboratory coats, gloves, eye/face protection

Facility Lab bench and sink

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EBSA pre-conference course, Basel, 18 June 2013

Biosafety Level II (BSL II)

Agents Known to cause diseases in healthy adultsTransmission: skin injuries, ingestion, mucous membrane exposure

Practices BSL I + limited access, biohazard sign, “sharps” precautions, Biosafety manual

Primary barriers

BSCs (biosafety cabinets) for splashes & aerosol producing procedures

PPE Laboratory coats, gloves, eye/face protection

Facility BSL I + autoclave available in facility

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Biosafety cabinets (BSC)

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EBSA pre-conference course, Basel, 18 June 2013

Biosafety Level III (BSL III)

Agents Indigenous / Exotic; serious / lethal diseaseTransmission by inhalatory exposure

Practices BSL II + controlled access, decontamination: all waste, all lab clothing

Primary barriers

BSCs for all manipulations

PPE Laboratory coats, gloves, eye/face protection +Respiratory protection

Facility BSL II + self-closing, double-door access; negative airflow into lab; entry airlock/anteroom

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Respiratory protection

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EBSA pre-conference course, Basel, 18 June 2013

Biosafety Level IV (BSL IV)

Agents Dangerous / exotic – high risk of aerosol transmission; frequently fatal infections; no vaccines / treatments

Practices BSL III + change clothing before entry & shower before exit; decontaminate all materials on exit

Primary barriers& PPE

Class III BSCs for all manipulations ORClass I / II BSCs + positive pressure suit

Facility BSL III + separate building; double-door autoclave, fumigation chamber, etc.

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BSL4 laboratories – separate buildings, high security, limited access (only authorized persons)

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BSL4 laboratories – bidirectional air filtration(HEPA filters retain particles ≤ 0.3μM)

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BSL4 laboratories: changing room (all clothing + decontamination shower)

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BSL4 – working area (double-door airlocks, waste decontamination by sterilization, vaccinated staff if vaccines

available, PPE: airtight pressurized suits, etc)

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BSL4 laboratories: decontamination shower upon exit

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CORRELATION: Risk group – BSL

Risk group BSL Facility

1 I Teaching laboratories

2 II Public health, Diagnostic laboratories

3 III Special diagnostic, Reference, Research laboratories

4 IV Dangerous pathogens units

The above correlation is orientative – BSL is decided based upon RISK ASSESSMENT for each type of laboratory procedure