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

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 Facilitator notes:

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 Facilitator notes:

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 Facilitator notes:

Role of microbiology laboratory in MDRO

MRSA found in Neonatal Intensive Care Unit 29.08.2016: first confirmed MRSA patient 03.09.2016: 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? Facilitator notes:

Role of laboratory in MDRO Facilitator notes:

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. Facilitator notes:

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) Facilitator notes:

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 Facilitator notes:

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. 2011 May 7. doi: 10.1111/j.1469-0691.2011.03570.x Reference: Magiorakos A P, Srinivasan A, Carey R et al Clin Microbiol Infect. 2011 May 7. doi: 10.1111/j.1469-0691.2011.03570.x

Microbiological laboratory methods

Sample processing workflow Facilitator notes:

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 Facilitator notes:

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 Facilitator notes:

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 Facilitator notes:

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 24-48 hours Facilitator notes:

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 Facilitator notes:

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) Facilitator notes:

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 Facilitator notes:

Antimicrobial susceptibility testing methods

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:

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 Facilitator notes:

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 Facilitator notes:

Antimicrobial susceptibility testing standards Standardization is necessary for aggregating and comparing data National committees EUCAST (http://www.eucast.org/) 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: http://www.eucast.org/

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:

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 Facilitator notes:

Rapid diagnostics Facilitator notes:

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): 1614-1620 Components of the actual turn-around time of a laboratory test

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:

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:

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. Facilitator notes:

Reporting of results

Reporting of results Who is the report aimed at? Timely notification Clinician Infection Control Public Health National Surveillance Timely notification Facilitator notes:

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 Facilitator notes:

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 Facilitator notes:

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 Facilitator notes:

National Surveillance Usually report retrospectively May compile through local public health or reference laboratory or directly from diagnostic laboratory Facilitator notes:

The role of the microbiology laboratory in outbreak investigtions

The role of the laboratory in outbreaks Early detection  cluster identification, novel mechanisms of resistance Investigation  typing Facilitator notes:

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:

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) Facilitator notes:

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) Facilitator notes:

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 Facilitator notes:

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:

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:

References Diekema DJ, Pfaller MA. Rapid detection of antibiotic-resistant organism carriage for infection prevention. Clin Infect Dis. 2013 June; 56(11):1614-20. 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. 2012 March; 18(3):268-81. Facilitator notes:

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

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