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Laboratory biosafety, infection prevention & control: PRIDA med micro course 2021
John FergusonHunter New England Health, Newcastle, NSW
2021 @[email protected]
Overview
1. Laboratory biosafety and infection control
2. Lab-acquired infection
3. Staff health / immunisation
4. Physical containment standards
5. Lab support for hospital infection control and surveillance
Laboratory biosafety considerations
Structure
• International Lab Quality Standard – ISO 15189
• Organisational management : biosafety officer
• Physical – PC2 and PC3 standards
• Training of staff – biosafety, awareness laboratory-acquired infection, infection control
• Staff immunisation requirements
Process
• Standard precautions: Hand wash/hygiene and PPE availability
• Standard operating procedures that account for safety risks
• Analysis of mishaps, lab acquired infections, risks
• Biosafety agenda item at every staff meeting – staff invited to identify hazards ; in-service training
• Staff health service / local doctor or health centre
Outcome
• Audits of biosafety and IC compliance (HH, PPE, dress codes)
• Environmental audits
• Waste management audits
Infection control: STANDARD PRECAUTIONS
Standard precautions: key assumptions
• Regard all samples are potentially infectious
• Ensure correct clothing/shoes/gown, routine eye protection and gloves
• Use safe practice and PPE to avoid any contact between bare skin and body substances
• Where necessary (e.g. Respiratory samples setups, blood culture subculture) use BSCII cabinet to avoid aerosol contamination
• Never smell an agar plate!
• Always clean hands after removal of PPE and prior to leaving the lab. for a break
• No eating or drinking in the lab! Avoid sucking pens or touching face.
Hand hygiene
Figure: Hand contaminated with MRSA post examination of a colonised patient. Right plate – hand print after alcohol rub – no growth!
• Technique – wash or alcohol rub – 6 steps (WHO)
• Gloves are NOT a substitute for HH
• Alcohol rub can also be used to check skin integrity – stinging indicates open cut – cover this with a waterproof dressing (band-aid)
6
PPE!
Laboratory infection hazards
https://www.researchgate.net/publication/291331348_Laboratory-Acquired_Infections_in_Belgium_2007-2012_An_online_survey/figures?lo=1
Lab acquired infection- potential pathogens
• Bacterial:– Tuberculosis
– N. meningitidis
– Brucella
– B. pseudomallei
– Enteric pathogens – Salmonella, Vibrio, Shigella
• Viral:– SARS-COV-2, Ebola, HIV, hepatitis A,B,C
• Fungal
• Parasitic– Heminths, Amoebiasis
Lab staff health
• Lab staff need education concerning lab-acquired infection and its prevention
• Lab management needs to monitor compliance with PPE, hand hygiene and ‘walk the talk’
• Each lab should have a biosafety officer who provides regular updates to staff and monitors PPE supply and other risks
• Educate re potential symptoms and the need to bring illness to the attention of the manager/ staff health service if exists
• Staff must not present to work with acute respiratory illness –covid-19 test required; consider TB if features suggest
• Immunisation
Lab staff immunisation considerations
• Hepatitis B – define each staff member’s status: if non-immune - need immunisation; if HbSAg carrier- may require antiviral treatment/assessment
• COVID-19 essential! • Influenza (annual) • Tetanus and pertussis booster every 10 years (dTpa)
• Hepatitis A - 2 doses provides long-term immunity ; can pre-screen serologically to detect prior immunity which is frequent in LMIC staff
• Varicella - document immunity as shown by either previous infection or vaccination. If negative -> vaccination advised.
• Neisseria meningitidis - optimally vaccination advised, ACWY and B conjugate vaccines (but expensive )
https://idmic.net/2016/03/02/hepatitis-a-to-e-josh-davis-with-some-clear-messages/
Compare/contrast – PC3 and PC4 standards
PC2 standard: required for micro labs.
Construction 5.3.3:
• Smooth, easily cleaned floors, no tiles.
• Secure access by authorised personnel only. Lockable when not in use. Keyless coded lock easiest.
• Separation of offices from lab space.
• Facilities outside lab for personal items
• Dedicated tea room and fridge .
• Sealed closed windows
PC2 standard: Ventilation – 5.3.4
PC2: Safety
• Class II (A or B) Safety Cabinet- monitored, regular filter change, serviced
• PPE provided and storage space for same
• Backflow prevention for water and gas.
• Eyewash and shower
• Chemical storage and fume hood for use
• Hand wash sinks
• Sharps disposal
PC2: Waste Disposal- section 12
• Liquid and solid waste containing micro-organisms and sharps must be decontaminated prior to disposal
• High temperature incineration for solid waste
• Autoclave for liquid waste
• After decontamination to be disposed of by relevant authority. Decontamination to be validated.
• Waste management SOP
• Regular auditing of compliance
Laboratory support for healthcare (hospital) infection prevention & control
• Educate clinicians re indications for testing
• Specify correct specimen collection protocols and indications– Screening samples – to detect multi-resistant organism colonisation
– Clinical samples – blood culture priority
– Environmental samples – only during outbreaks when approved
• Quality controlled culture and AST systems:– Reliably detect key multi-resistant organisms
– Prompt notification of critical results
• Timely reporting of results to clinicians and inf control; cumulative results – eg. antibiograms
Laboratory support IPC: surveillance of HAI
• Blood stream infections– Quality measures
• contamination < 3% of sets• volume of collection – weigh received bottles- > 80% adult bottles
should be above target volume (multiply weight by 1.05 to get volume)
– Significant isolates – categorise by: • Unique positive events – 14 day rule• HCA vs Community• Device associated – intravascular devices, indwelling UC, ventilator
associated• Clinical service / intensive care responsible• Procedure-associated – operations etc• Isolate type – MRSA, VRE, CPE, ESBL, species
– Outcome measures - mortality
Laboratory support IPC: surveillance of BSI
• Blood contamination:– Reduce contamination by asepsis during collection- training of
collectors very important
– For a list of potential contaminant species:
• Require two separate positive sets with the same isolate taken within 1 calendar day
• Examples – coagulase negative Staph. Bacillus, Corynebacterium, Propionibacterium species, Strep. Viridans group
• Track rates of contamination by service and location ; provide feedback to clinicians and collectors together with in-service training on correct practice
https://aimed.net.au/2018/08/09/blood-culture-surveillance-pathology-north-contamination-and-double-set-culture-rates/
Laboratory support IPC: surveillance of BSI
• Healthcare-associated:– Inpatient (event > 48 hrs after adm or within 48 hrs of discharge)– Inpatient, ICU-associated (event > 48 hrs after ICU adm or within 48 hrs of
ICU discharge)– Non-inpatient HCA
• IV device associated including haemodialysis associated• Procedure associated• Associated with prior surgery (up to 90 days for some surgical types ;
otherwise 30 days)• Associated with iatrogenic neutropenia
– Community by exclusion
• Intravascular device association:– IV device or access within prior 48 hrs– No other apparent source of BSI– Does NOT require evidence of exit site inflammation or a positive culture
from device tip
Laboratory support IPC: MRO surveillance
• Infections due to multi-resistant organisms (MRSA, VRE, ESBL, CPE, MDR/XDR TB)– Isolates from clinical (not screening) samples
– Subcategorise into sterile site (e.g. blood, CSF, pleural fluid) and non-sterile site
– Look for patterns – endemic or epidemic (outbreak) occurrence-
– Describe the epidemiology:
• Who, When, Where
• Epidemic curve
– Assist hospital with outbreak identification and control measures
Epidemiology is the “study of distribution and determinants of health-related states among specified populations and the application of that study to the control of health problems.”
https://idmic.net/2020/02/10/epidemiology-and-surveillance-101-tutorial-notes/
Laboratory support IPC: patient MRO screening & environmental cultures
• In general avoid culturing the environment for IC purposes-focus on screening and clinical samples as patients typically amplify MROs, esp. if receiving antibiotics which increases sensitivity of detection
• In the MRO outbreak setting (e.g. ICU ESBL or CPE ) :– Role for point prevalence and periodic patient screens (i.e. all patients
across the unit) to disclose the patient reservoir , allow for physical separation of colonised patients to reduce cross transmission & assess impact of control measures
– Staff screening of relevance for MRSA outbreaks on occasions
– One off environmental cultures to detect undisclosed reservoirs as suggested by epidemiological factors – new devices, reused patient equipment, hand wash sinks, moist items – humidifiers, cribs etc
Examination of organisms for clonality
• Phenotypic – species similarity, antibiogram, MALDITOF profile
• Genotypic – many methods– Restriction endonuclease typing (creates a banded ‘fingerprint’ for the
isolates)
– Whole genome sequencing
– Plasmid sequencing
Clonality implies a common source or cross transmission linked closely in time.
Example from E Timor 2020: 11 Bloodstream isolates of B. cepaciacomplex with similar antibiograms obtained from ICU patients –eventually tracked to contaminated unused imported central lines
Laboratory support IPC: Cumulative antibiogram production
• Significant, non screening clinical isolates
• First patient isolate from previous 12 months
• Quality controlled AST must be in place
• Separate antibiograms for urine and non-urine samples
• Separate listing of blood isolates with AST- key analyses:– Percent of Staph. aureus events that are due to MRSA (community vs
HCA)
– Proportion of Gram negative events resistant to gentamicin and ESBL (ceftriaxone resistance)
https://idmic.net/tag/antibiogram/
Example: 2018 PMGH, PNG
References – available via http://idmic.net
1. WHO Biosafety Manual Edition 4, 2020, abridged for Fleming Program
2. Information sheets
– Biosafety overview
– PPE
– Laboratory acquired infections
3. Online training:
– CDC (USA) Lab training site
– WHO GMPP modules (2.5 hrs)
An essential resource
CDC introductory biosafety modules
• CDC Lab training videoclasses – easy instructions on accessing | Microbiology and Infectious Diseases postgraduate teaching (PRIDA) (idmic.net)
• Highly recommended
WHO Good Microbiological Practices and Procedures (GMPP)
Estimated 2.5 hrs total time
Videos training link: https://www.who.int/activities/safeguarding-biosafety-and-
biosecurity-in-laboratories
1. PPE
2. GMPP - Pipetting
3. GMPP - Sharps
4. GMPP - Surface decontamination
5. GMPP - Autoclaves
6. GMPP - Workflow
7. GMPP - Transport