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Epidemiologicalpublic health role of the clinical microbiology laboratory

Last modified at 4/21/2016 7:25 PM by Vladimir Prikazsky

This public health/infection control role of the laboratory is essential for effective implementation and review of HAIs IC interventions and AS activities. The identification of HAIs is a field of joint activity between the clinical microbiologist, IPC professionals and physicians and nurses (i.e. it is a duty of care for all). While clinical staff will first note infection in individual patient, microbiologists will confirm the suspected or actual microbial causes. S/he will often be the first to identify possible clusters of infection in a ward or in different wards. This is particularly likely when these are caused by uncommon or particularly resistant bacteria. The microbiology laboratory is thus an essential part of an effective infection control programme. The ability of the medical microbiology laboratory to serve this second role is, of course, underpinned by its ability to fulfil the first role and provide standardised, rapid, accurate, precise and clinically relevant test results for infected/colonized patients.

The relevant activities are described in the following sections.

2.1 Surveillance.

2.1.1 Laboratory-based HAIs surveillance.

Laboratory-based ward liaison HAIs surveillance systems can, in theory at least be a convenient and cost effective way of identifying certain types of HAIs. The sensitivity and specificity of such surveillance will depend on whether specimens have been submitted to the laboratory. It is better for bloodstream and urinary tract infections, but for others e.g. lower respiratory tract infections, specimens are more often unavailable. Where the IC/HH team work closely with the clinicians, a protocol of systematic submission of specimens can be developed integrated with appropriate information, supplied on the specimen request forms. Unless this information is on the forms, then a visit or telephone communication with the relevant clinicians will be required. More often it is recognised that such systems are insufficient to inform IC and AS activities, but the data should still be included in more sophisticated HAIs surveillance. An integrated approach of patient-based surveillance with a continuous laboratory-based monitoring program is desirable.

2.1.2 Periodic reports.

Microbiology laboratory produce periodic reports (at least annually but e.g. in intensive care units over shorter periods) of isolated bacteria together with antimicrobial susceptibility data. Such reports have to be stratified by ward, anatomical site, patient group and pathogen and not include colonizing isolates (these can be analysed separately) and without duplicate isolates. Such data do not automatically mean causes of HAIs (see above), but are important as they show the burden for the hospital, and local epidemiology together with the trends of specific pathogen and specific resistance and a baseline incidence of particular microbes. Such reports are also locally important as a base for risk assessment and planning of preventive measures. In the laboratory based surveillance that is frequently used (see above), microbiological reports make a basis for case finding in wards. One does need to be cognoscente of the limitations, as well as the advantages, of using such systems.

2.1.3 Alert organism and condition surveillance systems.

There should be daily listings made available for, or urgent communication with, the IC/HH team of agreed alert condition e.g. cellulitis, and alert organisms. Alert organisms are mostly multi-antimicrobial resistant ones, but also rarer organisms with higher pathogenicity e.g. Panton-Valentine positive S. aureus, or high epidemic propensity, or new organisms and new resistances in that hospital. Specific examples include: Streptococcus pyogenes, antimicrobial resistant isolates e.g. methicillin-resistant Staphylococcus aureus (MRSA), vancomycin intermediate Staphylococcus aureus (VISA), vancomycin resistant enterococci (VRE), multidrug resistant (MDR) Pseudomonas aeruginosa, MDR Acinetobacter baumannii, MDR Mycobacterium tuberculosisClostridium difficile toxin-positive stool patients, extended spectrum beta-lactamase (ESBL) or carbapenem resistant Enterobacteriaceae (CRE), E.coliO127, Legionella spp, penicillin resistant (PR) Streptococcus pneumoniae etc.) as well as agents of bioterrorism or any other organism that could be of interest locally.

2.1.4 Active surveillance cultures.

Active surveillance cultures for alert (including multidrug resistant) organisms, is practiced by many hospitals throughout the world. This is mainly admission screening for MRSA, but many hospitals perform it also for ESBL Enterobacteriaceae, CRE and VRE. While admission screening for MRSA is a part of many guidelines (rules vary), screening for other resistant bacteria is still under consideration in many countries/regions, practices also varying in different hospitals depending on their local circumstances. The microbiology laboratory plays the essential role in this kind of surveillance, and can advise on the best media (including cheaper in-house media tailored to the local strains involved) and methods to be used and how the specimens are best collected. More rapid molecular methods may have a role to play depending on the clinical scenarios, occurrence of the organisms and cost effectiveness criteria used.

2.2. Outbreak investigations

The FEM WIKI discusses this in greater depth, including the various stages required to investigate clusters of cases of infection. Some of these clusters will be proven to be outbreaks. The laboratory serves several roles:  

  1. Early recognition. The first role of microbiology laboratory is early recognition of a cluster or outbreak. This can be achieved either through the laboratory information system which has incorporated an early warning system examining rates of test ordering or rates of positive isolates, or through routine observations at the bench and comparison with the baseline incidence. This requires the relevant skills amongst the laboratory/hospital staff.
  2. Immediate communication with ward and IC/HH staff.
  3. Further case finding (once case definitions have been agreed). After that the laboratory participates in further case finding (here there is a possibility to use specific selective media for isolation of the causative agent if it has some distinctive characteristics, e.g. the addition of specific antimicrobial(s) to the isolation media if the outbreak strain is resistant). If necessary the laboratory will process further specimens either from patients and staff (screening samples) or from the environment (e.g. food, water, instruments, devices).
  4. Identification of the causative agent. The isolated organism has first to be identified to the species level and susceptibility testing performed together, where relevant, with detailed analysis of resistance genes/plasmids. However, a microbial species may have several types that differ in some characteristics. Individual bacteria from the same species can differ up to 30% in their respective genomes and these genetic differences are not always phenotypically expressed. So it is a standard today to perform typing of microorganisms when microbes have been isolated from epidemiologically related patients.
  5. Typing (see typing and molecular biology sections). Typing of microorganisms is today one of the most important roles of microbiology in IC/HH. These growing needs have been highlighted in a conceptual model, showing laboratories with different capacities: national reference laboratories (national focal points), expert clinical laboratories with reference role, clinical laboratories with diagnostic and typing services and clinical laboratories with diagnostic services only. Usually, diagnostic laboratories routinely submit strains to reference laboratories for characterization and typing: a diagnostic laboratory should save isolates, especially from invasive infections but also from colonised patients/sites or, where relevant to the hypotheses to be tested, from the environment. However, over time, the distinction between diagnostic and reference laboratory functions has become less clear-cut due to the diffusion of molecular diagnostic methods. This progression poses several challenges, for example the need for standardization to ensure data comparability, but also the need to ensure there is a national central database which can record regional, national and international spread or emergence of important strains. Typing data may be able to confirm or refute hypotheses about possible sources and modes of transmission of the pathogen causing the outbreak.

The laboratory may also save patient serum samples if the causative agent is uncertain and there are the relevant serological assays available e.g. legionella spp outbreaks.

2.3 Antimicrobial stewardship (AS).

A major microbiology laboratory role is in the identification of aetiological agent of infection and in determining its susceptibility to antimicrobials for individual patient so the patient could be treated according to the individual agent susceptibility. But the role in AS is much broader and starts with the choice of antimicrobials for laboratory susceptibility testing. The panel of antimicrobials should be agreed with clinical teams and Antimicrobial Committee (team) and be based on periodic laboratory reports of antimicrobial susceptibilities of local isolates, stratified by pathogen, site of infection and by unit/service (e.g. susceptibility of isolates in chronic dialysis service might not be the same as in a surgical ward). Such reports are very important for the design of hospital antimicrobial formulary and hospital guide for empiric and definitive therapies and restrictive antimicrobial reporting and other agreed interventions. A medical microbiologist should usually be a member of AS Committee and antimicrobial team.

2.4 More specialised IC related services.

These can comprise microbial sampling from theatre, isolation wards, sterile preparation rooms (e.g. pharmacy) for routine or investigational analyses. Disinfection and sterilisation testing is covered elsewhere.

2.5 Participation in IC committee.

A clinical microbiologist should be a member of this committee as s/he is the specialist with the necessary competencies – educated to know characteristics of specific microorganisms pertaining to the pathogenicity, virulence, natural habitat, possible habitats in hospital, resistance to adverse conditions in environment, transmissibility and a way of transmission in hospital, resistance to disinfectants and antibiotics, that is all necessary for interpreting microbiological data for IC staff.

Besides this, using laboratory reports about isolated microorganisms, the clinical microbiologist is indispensable to the risk assessment process and planning of further activities in prevention and control of HAIs.

2.6 Education of IC, AS and clinical staff.

The microbiology laboratory staff should also serve as an important resource for the education of junior clinical microbiologists and laboratory technicians, but also of infectious disease specialists, other clinicians and pharmacists that are interested in AS and IC. This education can be formal (as a part of physician specialization/basic education for technicians and nurses) but also informal, during clinical rounds and daily communications regarding IC and AS. It is very important that such educational activities are agreed and documented e.g. they can be part of individual performance appraisals or personal development plans. This is even more vital where there is an off-site microbiology laboratory to ensure that such educational activities are still provided in all the hospitals served by the laboratory.

Such education is, of course, also important in the fields of biosafety. If this is not in place then HAIs can occur in the laboratory i.e. a health and safety at work incident. Laboratory personnel, as well as ward staff involved in obtaining and transport of biological specimens, are exposed to risk of infections. So it is important that all personnel involved are aware of such risks and that all pertaining biosafety standards are implemented to minimize the risk and audited regularly. Incidents need thorough investigation, a list of lessons learnt drawn up and any modifications made to SOPs/ward algorithms documented and a report sent to the IC Committee.

Link to European IC/HH Core Competencies: area 4 Infection control activities: Advising appropriate laboratory testing and use of laboratory data ICA 1-3


References are on the page The role of the clinical microbiology laboratory in infection prevention and control.

Original contribution from: 

Barry Cookson, University College London