Laboratory biosafety, infection prevention & control: PRIDA med micro course 2021

John FergusonHunter New England Health, Newcastle, NSW

2021 @mdjkfJohn.ferguson@health.nsw.gov.au

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