Field Epidemiology Manual Wiki

Stage 2 Systematically collecting information

Last modified at 12/20/2013 11:38 AM by Arnold Bosman

Identify basic facts about the disease and the aetiological agent from a standard reference text (ideally less than five years old). Examples include infectious disease textbooks such as: Heymann; Mandell; Topley and Wilson; Fields Virology (see references). There will be other key reference texts, including previous outbreaks and incidents,depending on the country and the disease. Sources on evidence-based medicine (see Appendix 3) are useful for checking what has already been done and to ensure that work is not repeated. Expertise on choosing reliablesources of information, such as bibliographic databases, websites and/or grey literature sources and advice on access to the full texts are usually available within Member States’ institution libraries. 

Checklist 2: Basic disease information/determinants

  • Occurrence: time, place and person
    • Geographical distribution: is disease endemic in country?
    • If not, what are routes of introduction, e.g. food/bird/animal/human?
    • Seasonal/temporal trends
  • Reservoir (if zoonotic, which species affected – will animals be symptomatic?)
  • Susceptibility: are specific risk groups at increased risk of exposure/infection, e.g.:
    • specific age groups (e.g. children, elderly);
    • occupational groups;
    • travellers;
    • those with impaired immunity, e.g. immunosupression/chronic disease; pregnant women;
    • others, e.g. as a result of specific recreational or other activities.
  • Infectiousness
    • Mode of transmission
    • Incubation period
    • Period of communicability
    • Length of asymptomatic infection
    • Reproductive rate 
  • Clinical presentation and outcome
    • Disease severity: morbidity; mortality; case fatality
    • Complications/sequelae 
    • Are specific risk groups at increased risk of severe disease/complications (consider children, elderly, those with immunosupression/chronic disease, pregnant women, occupational/recreational risks)
  • Laboratory investigation and diagnosis
    • Laboratory tests available
    • Test specifications (sensitivity, specificity, PPV, quality assurance) and limitations (crossreactivity, biosafety concern)
  • Treatment and control measures
    • Treatment (efficacy?)
    • Prophylaxis (vaccination/other)
    • Other control measures (e.g. quarantine, withdrawal of food product, culling animals)
  • Previous outbreaks/incidents
    • Novel transmission routes

Basic disease information from standard textbooks should be supplemented by searching published and grey literature (including outbreak reports and surveillance data, guidelines, disease fact sheets, etc). “A literature search should be a well-thought-out and organised search for all relevant literature published on a topic and is the most effective and efficient way to locate sound evidence on a subject”. (see When time and resources are limited, a preliminary literature search should be undertaken to identify the key literature in the subject area, however there will inevitably be a trade-off between time and sensitivity. Particular attention should be given to filtering the results,i.e. choice of subjects, timeframe, and restricting to ‘review’ articles – most citation databases offer the facility to filter searches in this way. A trained information specialist or librarian can help to identify the best way to use these options in databases and retrieve the appropriate records according to the questions. There are also sites available with tutorials and guides providing help with the literature search, such as the London School of Hygiene & Tropical Medicine Library (see for further information). It should be acknowledged that a comprehensive systematic review will not be possible in the early stages of a rapid risk assessment; however the need for such a review should be considered at a later stage when time and resources permit. 

Published literature

The key steps in an effective literature search include:

  • Clearly defining the question(s) and the type of information needed (e.g. type of studies searching for, any geographical/ethic/age limits)
  • Database(s) to be searched – Pubmed/Medline is universally available and access to Cochrane Library may also be free depending on the country agreement ( There are a range of citation databases that may also be used including Scopus, Web of Science, Google Scholar. For other databases, such Embase, which is specific to health, a subscription is needed. These databases vary in accessibility, geographical coverage, range and type of content (e.g. coverage of low-impact journals and conference proceedings). Ideally, more than one database should be searched and the results of each compared, however this is rarely practical in view of time restraints. It may be better to become proficient in using one database so that when an incident occurs a rapid literature search can be conducted. For further information see
  • Selection of search terms – text words and/or MeSH headings (best to use both if time permits).
  • Compiling search strategy and running the search – including use of Boolean operators (AND/OR).
  • Documenting search strategy and results.

Full articles should be used wherever possible rather than abstracts.

Further resources for effective literature searching are listed in the references (e.g. Member States public health services will often have their own resources and guides to doing literature searches.

Grey literature

These include key electronic publications such as ProMED and websites of national and international public health bodies (for outbreak reports and disease information). A list of suggested sources is included in Appendix 3. It will not be practical (or relevant) to search all of these in the early stages of a rapid risk assessment, however, as a minimum, the following should be searched:

  • Electronic publications, e.g. ProMED and WHO Disease Outbreak News for outbreak reports.
  • Key websites of the relevant national and international public health bodies to identify further disease information, guidelines, surveillance information, etc.
  • Additional outbreak reports may be available on the IHR and EWRS websites (restricted access) and can be identified through the relevant IHR NFP and EWRS NCP.