biological risk assessment for a microbiology laboratory

Risk Assessment in the Clinical Microbiology Laboratory

Nellie DumasBacteriology Laboratory

Wadsworth CenterNew York State Department of Health

Risk Assessment WebinarJune 15, 2011

Clinical Laboratory PRIORITIES

Safety

Accuracy

Timeliness

Lab-Acquired Infections in NYS 1999-2010

• E. coli O157

• Neisseria meningitidis

• Salmonella Typhi

• Campylobacter jejuni

• Brucella sp.

Biohazard Risk Assessment

CLEP Safety Sustaining Standard of Practice 1: Biohazard Risk Assessment and Biosafety Program

Minimize risk for lab-acquired infections by addressing:

• Aerosol-generating specimen/culture procedures (e.g., vortexing, centrifuging, pipetting, mixing)

• Contamination / Cross-contamination potential

• Sharps


• Identification of hazardous characteristics of agents worked with in lab

• Identification of lab procedure hazards: agent concentration, suspension volume, equipment, aerosol-generating procedures, use of sharps

• Determine appropriate biosafety level and select additional precautions

• Evaluate proficiency of staff regarding safe practices and safe operation of equipment

• Review risk assessment with a biosafety professional

Clinical specimen types known to be potential sources for agents of laboratory-acquired infection

Specimen Type Agents that could be presentBlood HBV, HCV, HIV, SARS, WNV, Brucella, N. meningitidis, Francisella,

Enteric pathogens, B. pertussis, Leptospira, other select agents such as B. anthracis, Y. pestis, Burkholderia mallei and B. pseudomallei

Serum WNV, Botulism toxin, HBV, HCV, HIV

CSF HBV, WNV, HIV, Brucella, N. meningitidis, Francisella, M. tuberculosis, B. anthracis, Y. pestis

Saliva N. meningitidis, HBV, HIV

Urine HBV, HIV, SARS, Brucella, Francisella, Salmonella, STEC, M. tuberculosis, Y. pestis, Leptospira, B. anthracis

Feces Salmonella, Shigella, Campylobacter, Y. pestis, Vibrio species, H. pylori, STEC, HBV, SARS, Polio virus, B. anthracis, Botulism toxin

Semen Brucella, HBV, HIV

Nasopharyngeal N. meningitidis, B. pertussis, C. diphtheriae, H. pylori, Polio virus, SARS, HBV

Respiratory sites SARS, Brucella, B. anthracis, M. tuberculosis, B. pertussis, Legionella, Francisella, Burkholderia mallei, B. pseudomallei, Y. pestis

Tissues SARS, Polio virus, WNV, Brucella, M. tuberculosis, Campylobacter, Leptospira, B. mallei, B. pseudomallei

Gastric lavage M. tuberculosis, H. pylori

Wound/Skin lesion exudates Francisella, B. anthracis, Burkholderia mallei, B. pseudomallei

Biorisk characteristics of viruses reported to cause laboratory-acquired infections

Biological Agent

Infective Dose

Potential mode of transmission

RecommendedContainment

Hepatitis B 108-109 particles/ml Percutaneous or mucocutaneous

BSL-2 for handling body fluid and tissue specimens

Hepatitis C 102-103 particles/mlPercutaneous, rarely

mucocutaneousBSL-2 for handling body fluid and

tissue specimens

HIV 100-104 particles/mlPercutaneous or mucocutaneous

BSL-2 for handling body fluid and tissue specimens

Influenza Viruses Varies by strain Inhalation of aerosols; mucocutaneous

H1N1: Splash protection if performing rapid immunoassay; biosafety cabinet

if performing IFA, DFA, culture or molecular assays

HPAI: requires BSL-3 conditions

SARS-Corona virus Unknown Inhalation of aerosols Untreated specimens processed in biological safety cabinet

West Nile Virus UnknownInhalation of aerosols;

percutaneous or mucocutaneous

BSL-3 for manipulation of cultures

Biorisk characteristics of bacteria reported to cause laboratory-acquired infections

Biological Agent

Infective Dose Potential mode of transmission


Brucella species 10 to 100 orgs Inhalation of aerosols BSL-3 for manipulation of cultures

Campylobacterspecies

500 orgs or less Ingestion due to cross-contamination

BSL-2

Coxiella burnetii 10 orgs Inhalation of aerosols BSL-3 for manipulation of cultures

Escherichia coli O157:H7

10 to 100orgs Ingestion due to cross-contamination

BSL-2

Francisellatularensis

Aerosols: 5 to 10 orgs

Ingestion: 108 orgs

Inhalation of aerosols BSL-3 for manipulation of cultures

Biological Agent

Infective Dose

Potential mode of transmission


Mycobacterium tuberculosis

1 to 10 orgs Inhalation of aerosols BSL-3 for manipulation of cultures

Neisseriameningitidis

Not known Inhalation of aerosols Sterile site isolates should be manipulated in biological safety

cabinet

Salmonella species

105 to 109

orgsIngestion due to cross-

contaminationBSL-2 for non-typhi; BSL-3

recommended for manipulation of Salmonella Typhi if aerosols are likely

Shigella species 10 to 100 orgs Ingestion due to cross-contamination

BSL-2

Staphylococcus aureus

Virulence varies greatly

between strains

Inhalation of aerosols; percutaneous or mucocutaneous

BSL-2

Biorisk characteristics of bacteria reported to cause laboratory-acquired infections

Protect from Aerosol and Cross-contamination Transmission

Always work with suspect specimens in BSC (ref: BMBL5 Agent Summary Statements):

• Neisseria meningitidis!!!!!!!!!• Salmonella Typhi• Shiga toxin-producing E. coli• Shigella• B. anthracis, Brucella, B. mallei,

B. pseudomallei, F. tularensis, Y. pestis

High Risk Procedures for High Risk Agents

Outside of Biosafety Cabinet

• Opening culture plates• Picking colonies off culture plates• Vortexing tubes • Setting up automated identification

systems• Performing catalase• Performing oxidase• Performing motility test


Method or Procedure:• Risk Factor(s)• Probable route(s) of transmission• Required practices, primary barriers, and

safety equipment• Triggers for implementation of enhanced

precautions for high risk agents• Required enhancements in practices,

primary barriers, or safety equipment

Aerosol-generating Procedures

• Vortexing

• Centrifuging

• Pipetting

• Mixing

• Grinding

• Blending

• Automated system preparations

• Fixing slides with a flame

• Taking off disposable gloves improperly

Risk assessment of laboratory activitiesLaboratory activity Causes

aerosolsPotential

for splashes

Potential for

ingestion due to

splashes

Potential for skin

inoculation

Processing primary specimens

Removing caps or swabs from culture containers Yes Yes Yes

Grinding tissues Yes

Blending food specimens Yes

Centrifuging Yes

Pouring or decanting fluids Yes Yes Yes

Using needles or syringes:

Aspirating fluid from a sealed bottle Yes Yes

Withdrawing needles from stopper Yes Yes

Inoculating culture plates with fluid from a syringe Yes Yes Yes

Disposal of contaminated sharps Yes

Laboratory activity Causes aerosols

Potential for

splashes

Potential for

ingestion due to

splashes

Potential for skin

inoculation

Bacterial suspensions

Using a swab to make a bacterial suspension Yes Yes Yes

Vortexing , sonicating Yes Yes Yes

Aspirating bacterial suspension with pipette Yes Yes Yes

Using autoinoculater for automated identification systems

Yes Yes Yes

Inoculating identification cards using vacuum system Yes

Inoculating suspension onto plate with a swab Yes Yes Yes

Risk assessment of laboratory activities

Laboratory activity Causes aerosols

Potential for

splashes

Potential for

ingestion due to

splashes

Potential for skin

inoculation

Manipulating bacterial culture plates

Opening plate to observe growth Possibly

“Sniffing” plate as part of bacterial identification Yes

Using inoculation loops:

Flaming loop with bacterial growth on it Yes

Cooling loop in culture plate Yes

Manipulating bacterial growth with hot loop or needle Yes Yes

Disposal of specimens and culture plates

Roughly discarding bacterial suspensions Yes Yes Yes

Roughly discarding culture plates or specimens into receptacle

Yes Yes Yes

Risk assessment of laboratory activities

Procedure Hazards & Controls

Risk Factor(s) Hazards Required practices and safety equipment

Triggers for implementation of

enhanced precautions

Required enhancements in practices and safety

equipment

Removing caps or swabs from culture containers

Aerosols/droplets, splashes

Handle and process specimen with facial barrier (BSC, face or bench shield), lab coat, disposable gloves

Suspect botulism specimens

Suspect select agents

Mouse Bioassay – use animal testing PPE & handling SOP

Suspect select agents – deliver to Biodefense Lab

Grinding tissues Aerosols/droplets Same as above Same as above Same as above

Blending food samples

Aerosols/droplets Same as above Same as above Same as above

Centrifuging Aerosols/droplets Same as above; use capped cups and open in BSC

Same as above Same as above

Pouring or decanting fluids


Same as above Same as above Same as above

Method or Procedure: Processing primary specimens




Required enhancements in

practices and safety equipment

Aspirating fluid from a sealed bottle

Aerosols/droplets, percutaneous

Handle and process specimen with facial barrier (BSC, face or bench shield), lab coat, disposable glove; use safe sharps practices; do not recap; use sharps disposal container

Suspect botulism specimens


Mouse Bioassay – use animal testing PPE & handling SOP

Suspect select agents –deliver to Biodefense Lab

Withdrawing needles from stopper

Aerosols/droplets, percutaneous


Inoculating culture plates with fluid from a syringe

Aerosols/droplets, splashes, percutaneous


Disposal of contaminated sharps

Percutaneous Follow sharps handling and disposal SOP; do not recap; use sharps disposal container



Method or Procedure: Using needles or syringes





Required enhancements in

practices and safety equipment

Using a swab to make a bacterial suspension


Perform initial testing of unknown Gram negs in BSC until SA R/O; wear appropriate PPE


Suspect N. meningitidis

Suspect select agents –deliver to Biodefense Lab

Suspect N. mening/use BSC

Vortexing, sonicating Aerosols/droplets, splashes

Perform in BSC; use capped/enclosed materials; allow settling time


Aspirating bacterial suspension with pipette


Perform initial testing of unknown Gram negs in BSC until SA R/O; wear approp PPE


Using autoinoculaterfor automated identification system


NA NA NA

Inoculating identification cards using vacuum system

Aerosols/droplets NA NA NA

Inoculating suspension onto plate with a swab



Method or Procedure: Bacterial suspensions





Required enhancements in practices and safety

equipment

Roughly discarding bacterial suspensions


Place carefully in bleach/biohazard bag bucket on bench

Any suspensions made in BSC

Carefully discard in bleach/biohazard bag in BSC; follow SOP for bag disposal

Roughly discarding culture plates or specimens


Place carefully in biohazard bag/autoclave stock pot

Any culture plates within BSC Carefully discard in bleach/biohazard bag in BSC; follow SOP for bag disposal

Method or Procedure: Disposal of specimens and culture plates

Primary specimens for bacterial culture

Inoculate culture plates wearing lab coat and gloves and face shield, or inside biological safety cabinet

Growth of gram-negative

diplococcisuggestive of

Neisseria meningitidis

Work in BSC until Neisseria meningitidis

is ruled out

Source: Respiratorysite or sterile site such

as blood or CSFSlow-growing colonies

on blood agarGram stain:

gram-negative coccobacilli

Any specimen source

Work in BSC

Oxidase –Urea –

No hemolysisNo pigment

Rule out Francisellatularensis

Oxidase +Urea +

No hemolysisNo pigment

Rule out Brucella sp.

Other bacterial growth

Work on bench top

usingappropriate

sterile technique

Primary specimen received with request to test for or

confirm any of the following:

Bacillus anthracisBrucella species

Burkholderia malleiBurkholderia pseudomallei

Coxiella speciesFrancisella species

Q-feverRickettsia prowazekiiRickettsia rickettsii

Yersinia pestis

Begin work in BSL-3 facilityuntil select agents are

ruled out

Flowchart for processing primary specimens

Biorisk Assessment

Establish a PPE Program, including

• Use of Biosafety Cabinet

• Use of Facial Barriers

• Appropriate Use of Disposable Gloves

Biosafety Containment Risk Assessment

Recommended Use of Biosafety Cabinet includes::

• Primary specimen handling/processing

• Aerosol-generating procedures

• Open capped centrifuge cups in BSC

• All vortexing: Use closed items only

(Allow settling time before opening or manipulating vortexed material)

Disposable Gloves

• Caution should be observed in removing gloves: Snapping or stretching gloves may result in aerosol formation!

• Immediate glove removal upon leaving each work station is intended to prevent inadvertent contamination of communal objects (e.g., phones, pens, keyboards, etc.)

Clinical Microbiology Lab Reality

Budgetary Issues:• Space constraints - new technologies to

reduce exposure potential, but no space• PPE – off brands; inferior grade; use of

appropriate PPE reduces risk, but does not eliminate (staff training!)

• Laboratory equipment –upgrading/replacing existing equipment; maintenance contracts


Education/Training:

• Trigger points!!

• Indicate when work should be performed in BSC

• How to properly perform tasks in BSC

• Annual risk assessment – clearly identifies potential aerosol and exposure operations


Suspect/Unknown Specimens:

• Perform within your risk assessment reality!

• Perform testing within your capability!

• Slow-growing organisms - FLAGS

• PT specimens - FLAGS

• Select agents – rule/out and refer - FLAGS

Clinical Laboratory PRIORITIES

Safety

Accuracy

Timeliness

Contact Info

• Nellie Dumas: [email protected]

• Christina Egan: [email protected]

• David Hill: [email protected]

biological risk assessment for a microbiology laboratory

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