1. Facilitator notes:
Control of Multi-Drug Resistant Micro-organisms in Health Care Settings
Session 2a: The central role of the laboratory in surveillance and outbreak management
Version: 10 April 2018

2. Objectives
Critically evaluate the clinical effectiveness and costs effectiveness of currently available laboratory based MDRO tests
Discuss the importance of the rapid and accurate communication of laboratory results to key personnel involved immediate patient management
Critically review the clinical importance of quality and safety issues surrounding current laboratory practice
Demonstrate an ability to communicate and report effectively with public health departments related to the management of MDROs
Critically appraise the role of the diagnostic laboratory in outbreak management
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3. Objectives
Critically analyse the principles of infection prevention and control practices in relation to MDRO in a hospital setting
Critically review the evidence base for local policies and protocols including preventative strategies
Demonstrate the importance to MDRO of preventing all hospital acquired infections
Critically evaluate the effectiveness of different interventions in minimizing the transmission of MDROs
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4. Outline This session consists of the following elements:
Introduction to the role of microbiology laboratory in MDRO and outbreak investigations
Explanation of the microbiological laboratory methods, antimicrobial susceptibility testing standards and reporting of results
Group exercise integrating current laboratory practices, challenges and solutions
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5. Role of microbiology laboratory in MDRO

6. MRSA found in Neonatal Intensive Care Unit
: first confirmed MRSA patient
: three new MRSA patients
Screening and retrospective testing identifies 17 more:
2014: 11; 2015: 15; 2016: 28
Identified that all isolates are spatype T127
Common type – do we need even more information?
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7. Role of laboratory in MDRO
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8. Are we all the same? Is there one model for everyone?
In Europe:
Countries with/without microbiology as a recognized speciality
Hospital laboratories, private laboratories
National microbiology reference laboratory or reference laboratory by organism or resistance type
National or regional organization
Prevalence of organisms and ability to handle outbreaks are highly variable
In all cases the laboratory has a central role.
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9. Requirements from laboratory
Clinical requirements from laboratory
Rapid diagnosis with clear guidance for treatment
Organism identification to species level and sensitivity results
Infection Control requirements
Early identification of outbreaks/incidents
Subtyping of organisms sufficient to confirm true cross infection/outbreak
Public Health Surveillance requirements
Consistent methods of collection, analysis and reporting of results
A small error (e.g., over-diagnosis by 5% does not matter as long as it is consistent)
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10. Factors influencing laboratory investigation
Clinical suspicion
Quality and type of sample
Speed of transfer to laboratory
Information provided with request
Laboratory methods of detection
Susceptibility testing methods
Available resources
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11. ECDC definitions of MDRO
Multidrug-resistant (MDR) – non-susceptible to at least one agent in > three antimicrobial categories Extremely drug-resistant (XDR) – non-susceptible to at least one agent in all but two or fewer antimicrobial categories Pandrug-resistant (PDR) – non-susceptible to all agents in all antimicrobial categories These categories vary for each species and exclude known intrinsic resistance.
Facilitator notes:
Reference: Magiorakos A P, Srinivasan A, Carey R et al Clin Microbiol Infect May 7. doi: /j x
Reference: Magiorakos A P, Srinivasan A, Carey R et al Clin Microbiol Infect May 7. doi: /j x

12. Microbiological laboratory methods

13. Sample processing workflow
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14. Detection of organisms by laboratory methods
Microscopy
Bacterial culture
Serology for antigens/antibodies - not considered further
Molecular testing methods - Polymerase chain reaction (PCR)
Mass Spectrometry - MALDI-TOF MS
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15. Bacterial Culture Requires sufficient number of organisms
Requires selection of appropriate media
May require selective media
Must know clinical history to direct culture methods appropriately
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16. Bacterial Culture (2) Traditional method Retains central role
Dependent on quality of sample
Collection
Transport
Timeliness
Important to be aware of limitations of each sample
type
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17. Bacterial culture (3) Advantages Low cost of materials
Further investigations possible
Limitations
Insensitive
Labour intensive
Will miss pathogens if antibiotics already received
May report wrong organism
Results take hours
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18. Polymerase chain reaction (PCR)
Detect key DNA/RNA sequences
presence of organism, even after antibiotics / at subclinical levels
Must have necessary primers to detect suspected pathogens
Result may be available in one hour
Automated systems
require expensive capital equipment but can batch process specimens, less labour intensive
Introduces option of near patient testing (e.g., screening for MRSA, C. difficile)
Have to culture all positive samples to confirm result and perform sensitivity testing
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19. Typing and subtyping of organisms
Required to identify linked cases/clusters/outbreaks (same or closely associated strains)
Usually undertaken by specialist/reference laboratories
Must be discriminatory
Too insensitive - cannot differentiate between strains
Too sensitive - cannot detect linked strains (clusters)
Must be relatively stable over time
Ribotyping – C. difficile
Phage typing – Salmonella typhimurium
Whole genome sequencing (WGS)
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20. MALDI - TOF MS
Matrix Assisted, Laser Desorption Ionization, Time of Flight Mass Spectrometry
Identifies organisms once isolated in culture from pattern of the mass spectrum in 6-10 minutes
Systems in development to identify organisms during growth phase (e.g., linked to BACTEC)
Direct identification in blood cultures routinely used
Increased workflow efficiency
Cost reduction
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21. Antimicrobial susceptibility testing methods

22. Antimicrobial susceptibility testing
Requires pure culture
Aims:
to detect phenotypic sensitivity profile (not all resistance genes are expressed)
to detect inducible resistance
Key characteristics:
to measure susceptibility of an isolate to range of antibiotics at the individual patient level for effective prescribing
to assess emerging bacterial resistance patterns data used to revise standard prescribing policies
Facilitator notes:

23. Requirements of antimicrobial sensitivity testing methods
Reproducible
Detect phenotypic resistance (e.g., MRSA)
Detect presence of resistance determinants that are transferable (e.g., ESBLs, Carbapenemases)
Comparable between laboratories and across countries to allow reliable surveillance to detect emerging resistance
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24. Antimicrobial susceptibility testing methods
Broth dilution
Antimicrobial gradient (e.g., E-test)
Disc testing
Measure zone size - labour intensive and can be very accurate but
prone to operator error
Automated systems
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25. Antimicrobial susceptibility testing standards
Standardization is necessary for aggregating and comparing data
National committees
EUCAST (
harmonise standards for breakpoints from all European National breakpoint committees
adopted across the ECDC as the preferred method - it will allow consistency of reporting and comparison between member states
Facilitator notes:

26. Limitations of antimicrobial susceptibility testing methods
carried out in controlled environment
some resistance genes are not expressed phenotypically
Minimum inhibitory concentration (MIC) breakpoints are based on the pharmacokinetics of the antibiotic but these depend on the clinical conditions of the patient and the site of the infection
indicates a PROBABILITY of successful treatment
needs to be interpreted in the context of
the clinical status
the nature of the infection
the pharmacokinetics/dynamics of the agent
Facilitator notes:

27. Novel approaches in antimicrobial susceptibility testing methods
Real-time PCR
DNA-microarrays: detect many resistance genes
MALDI-TOF MS: detect carbapenemase activity in 1-4 hours – even if the causative enzyme is unknown
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28. Rapid diagnostics
Facilitator notes:

29. Components of the actual turn-around time of a laboratory test
How rapid is rapid?
Facilitator notes:
Source: Diekema DJ. Clin Infect Dis. (2013) 56 (11):
Components of the actual turn-around time of a laboratory test

30. Changing the clinical microbiology laboratory
Core (centralized) laboratory
Concentrates samples from many facilities
Lower costs
Delayed reporting
Point-of-care laboratory (POCL)
Rapid diagnostic tests within 4 hrs
Operator-independent tests
Syndrome based kits
Automation
Facilitator notes:

31. Reference laboratory functions for MDRO
A reference laboratory for monitoring antimicrobial resistance should provide the following services to supplement phenotypic resistance data:
Confirmation of phenotype and identification of resistant organisms
Identification and characterisation of resistance mechanisms
Typing of resistant organisms to species/sub-species level
Evaluation of methods and supporting diagnostic laboratories
Facilitator notes:

32. Quality standards of laboratory
Laboratory should quality assure activities
Users should be aware of standards
Internal quality assurance
External quality assurance
Laboratory Accreditation
Compliance with Health and Safety regulations – Appropriate containment level usually 2 and 3.
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33. Reporting of results

34. Reporting of results Who is the report aimed at? Timely notification
Clinician
Infection Control
Public Health
National Surveillance
Timely notification
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35. Clinician
Need to get report to appropriate ward when clinician will act on it
Phone urgent results (e.g., cerebrospinal fluid film any time)
Phone other results when clinician available to act
Electronic reporting - need to flag positive results
Paper reports
need to get to clinician at appropriate time of day to act
not always easy - laboratory transport systems often dependent on other hospital priorities
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36. Infection Control
Need to get information to appropriate infection control personnel
Phone urgent results to on-call Infection Control team
Discussion of appropriate infection control interventions
Paper reports - audit trail should be in place
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37. Public Health Frequency of reporting
Immediate - confirmed meningococcal meningitis
Within 24 hours - suspected outbreak (e.g., Salmonella)
Weekly - standard reports from which Public Health compile trends
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38. National Surveillance
Usually report retrospectively
May compile through local public health or reference laboratory or directly from diagnostic laboratory
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39. The role of the microbiology laboratory in outbreak investigtions

40. The role of the laboratory in outbreaks
Early detection  cluster identification, novel mechanisms of resistance
Investigation  typing
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41. Typing in outbreak investigation
Goal: to establish clonal relatedness and distinguish unrelated strains originating from other sources
Methods:
Phenotypic  e.g., antimicrobial resistance
Molecular  e.g., PCR, pulsed-field gel electrophoresis (PFGE), WGS
Reference laboratory
Epidemiological information remains indispensable
Facilitator notes:

42. Investigation of emerging AMR
Identify clonal spread
Identify resistance mechanism
Reasons for emergence
e.g., foreign travel, establishment within hospital population, nursing home or other institutions, general population
implications for control measures
Review control measures (e.g., infection control, antimicrobial prescribing policies)
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43. Challenges for the modern microbiology laboratory
Quality assurance
Standardization
Communication
Timely identification and susceptibility testing
Communication with clinical team, infection control, public health, reference laboratories
Resource planning
Investment in and adoption of new technologies (MALDI-TOF MS, genomics)
Involvement in planning of surveillance activities (e.g., passive vs. active)
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44. In summary List of learning points in this session:
The role of the laboratory is pivotal in all aspects of MDR infections
Bacterial culture is the mainstay but new automated systems are improving identification and turnaround
Users must be familiar with the advantages and limitations of the various methods
Systems must be in place to quality assure laboratory activity
The quality of a report produced by a laboratory is dependant on the quality of sample and information submitted
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45. Plenary feedback
Opportunity for group activity and discussion around laboratory investigative methods in each member state to be fed back in a plenary session.
Facilitator notes:

46. Group exercise Key areas:
Current laboratory practices in member states, identifying common practice
Implementation of a standardized approach towards susceptibility testing in the member states of European Union
Different mechanisms of reporting to public health
Challenges and solutions
Facilitator notes:

47. References
Diekema DJ, Pfaller MA. Rapid detection of antibiotic-resistant organism carriage for infection prevention. Clin Infect Dis June; 56(11):
Magiorakos AP, Srinivasan A, Carey R, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect March; 18(3):
Facilitator notes:

48. Facilitator notes:
Acknowledgements The creation of this training material was commissioned in 2011 by ECDC to Health Protection of Scotland, National Services Scotland, University of Chester and University of Dundee with the direct involvement of Eastaway A, C Wiuff, A Seaton, J Reilly, M Rivett, P Davey, A Bryan, D Robertson. Adapted / modified by: S. Rosales Klintz, Karolinska Institutet, Stockholm, Sweden, 2015, ECDC MDRO course Diamantis Plachouras, ECDC, 2015, ECDC MDRO course Oliver Kacelnik, Norwegian Institute of Public Health, 2016, ECDC MDRO course The revision and update of this training material was commissioned in 2017 by ECDC to Transmissible (Netherlands) with the direct involvement of Rita Szabo, Remco Schrijver and Arnold Bosman

49. This work is licensed under the Creative Commons (http://creativecommons.org)
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Author: Dr Anne Eastaway, C Wiuff, A Seaton, J Reilly, Miss Michelle Rivett, P Davey, A Bryan, D Robertson (2011)
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Adapted / Modified by:
S. Rosales Klintz, Karolinska Institutet, Stockholm, Sweden, 2015, ECDC MDRO course
Diamantis Plachouras, ECDC, 2015, ECDC MDRO course
Oliver Kacelnik, Norwegian Institute of Public Health, 2016, ECDC MDRO course
Rita Szabo, Remco Schrijver in collaboration with Transmissible (Netherlands), 2018
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