Advanced Field Epi:Manual 1 - Disease Investigation/en - Revision history

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 [[Image:Theoretical studies.svg]]
-{{example|For example, simulation models of the spread of FMD have been used to help understand the behaviour of the 2001 outbreak in the UK and to predict the potential impact of alternative control strategies ([#_ENREF_19 Morris et al., 2001])}}
+{{example|For example, simulation models of the spread of FMD have been used to help understand the behaviour of the 2001 outbreak in the UK and to predict the potential impact of alternative control strategies ([#19 Morris et al., 2001])}}
 '''Characteristics, strengths and weaknesses of main study types (adapted from Thrusfield, 1995)'''

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 * If the RR is less than 1 and is associated with a significant p-value or if the 95% confidence interval for the RR does not include 1, then the risk factor is associated with a reduced risk of disease. Often factors with a RR less than one are called ''protective risk factors'' because they are associated with a reduced risk of disease.
-The numeric value of the RR is a measure of the strength of association between the risk factor and disease. If possible the 95% confidence interval for the RR should be examined. If the confidence interval does not overlap one then we can be more confident that the association may be meaningful. A statistical test and p-value will provide similar information â€“ telling you whether the RR is statistically different to one.
+The numeric value of the RR is a measure of the strength of association between the risk factor and disease. If possible the 95% confidence interval for the RR should be examined. If the confidence interval does not overlap one then we can be more confident that the association may be meaningful. A statistical test and p-value will provide similar information - telling you whether the RR is statistically different to one.
 Note that the RR alone does not provide evidence of causality. It provides a measure of statistical association. Additional information is required before we can determine that a particular risk factor may be causal for a particular disease.

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 Data and information may also be obtained from talking to producers or other people, from the literature review, from government statistics on animal production and laboratory testing (including iSIKHNAS data).
-{{example|Information gathered in looking at salmonellosis in sheep feedlots may come from a literature search, from which it is concluded that Salmonella is orally acquired and exposure dose is important â€“ this may lead to identification of simple measures such as feeding in raised troughs which prevent faecal contamination of feed and ensuring good drainage to prevent slurry build-up. Alternatively, data might be available from feedlot and veterinary records, providing facts about cases (and non-cases) of salmonellosis that have occurred. This data would then need to be collated, summarised and interpreted to generate information from which to draw conclusions.}}
+{{example|Information gathered in looking at salmonellosis in sheep feedlots may come from a literature search, from which it is concluded that Salmonella is orally acquired and exposure dose is important - this may lead to identification of simple measures such as feeding in raised troughs which prevent faecal contamination of feed and ensuring good drainage to prevent slurry build-up. Alternatively, data might be available from feedlot and veterinary records, providing facts about cases (and non-cases) of salmonellosis that have occurred. This data would then need to be collated, summarised and interpreted to generate information from which to draw conclusions.}}
 For an outbreak investigation, relevant data could include quantitative data on individual cases of disease, case histories on individual animals (both cases and non-cases) veterinarians' (or others) observations and impressions on cases, laboratory reports on testing undertaken on affected and unaffected animals, as well as potential sources of disease (such as samples of feed, water, soil and environment).

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	'''Number of animals per group to examine to determine if a particular finding is more common in cases than non-cases (95% confidence, 80% power, equal sizes for case and non-case groups and assuming a two-tailed test.'''		'''Number of animals per group to examine to determine if a particular finding is more common in cases than non-cases (95% confidence, 80% power, equal sizes for case and non-case groups and assuming a two-tailed test.'''

−	[[Image:Sample size calculation matrix.~~svg~~]]	+	[[Image:Sample size calculation matrix.jpg]]

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 Some of the commonly used, web-based, scientific databases include:
-* Medline/PubMed â€“ This indexes all major medical, veterinary, epidemiological and associated journals, and is freely available for all users through PubMed ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi http://www.ncbi.nlm.nih.gov/entrez/query.fcgi]).
+* Medline/PubMed - This indexes all major medical, veterinary, epidemiological and associated journals, and is freely available for all users through PubMed ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi http://www.ncbi.nlm.nih.gov/entrez/query.fcgi]).
 * Medline is also available through Current Contents and other service providers through institutional library subscriptions.
 * ScienceDirect ([http://www.sciencedirect.com/ http://www.sciencedirect.com/]) provides indexing and search facilities for a wide variety of scientific journals in the physical, life, health and social sciences.
 * Biosis previews/Web of knowledge ([http://thomsonreuters.com/products_services/science/science_products/a-z/biosis/ http://thomsonreuters.com/products_services/science/science_products/a-z/biosis/]) indexes a wide variety of journals, conference proceedings, books, review articles etc in the broad life sciences area. Available through institutional subscription.&nbsp;
-* Sciverse Scopus ([http://www.scopus.com/home.url http://www.scopus.com/home.url]) claims to be the worldâ€™s largest abstract and citation database of peer-reviewed literature and quality web sources, covering a multitude of topics. It is available through institutional subscription and some publishers provide temporary access to reviewers of journal papers.
+* Sciverse Scopus ([http://www.scopus.com/home.url http://www.scopus.com/home.url]) claims to be the world's largest abstract and citation database of peer-reviewed literature and quality web sources, covering a multitude of topics. It is available through institutional subscription and some publishers provide temporary access to reviewers of journal papers.
 * Agricola ([http://agricola.nal.usda.gov/ http://agricola.nal.usda.gov/]) is the catalogue of the National Agricultural Library of the USA and provides citations and abstracts for an extensive collection of agricultural literature.
 * CAB Abstracts (CAB Abstracts&nbsp;) includes over 6.3 million records&nbsp;from 1973 onwards, with over 300,000 abstracts added each year, covering agriculture, environment, veterinary sciences, applied economics, food science and nutrition. Access is via institutional subscription or by time-based payment.

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 |}
-{{example|From the above results, and with reference the above table, Organism 2 is the only one which is statistically associated with an animal being a case, despite Organism 3 being isolated more frequently from cases. The reason for this conclusion is that the sample size of 30 is insufficient to detect a statistical difference in the isolation rates from cases and non-cases for Organisms 1 and 3, but is sufficient for Organism 2. This does not â€œproveâ€ that Organism 2 is the primary pathogen (as it could be an opportunistic, secondary invader), but by examining a reasonable number (in this case, 30) of cases and non-cases we are much better able understand the relative importance of the three organisms.}}
+{{example|From the above results, and with reference the above table, Organism 2 is the only one which is statistically associated with an animal being a case, despite Organism 3 being isolated more frequently from cases. The reason for this conclusion is that the sample size of 30 is insufficient to detect a statistical difference in the isolation rates from cases and non-cases for Organisms 1 and 3, but is sufficient for Organism 2. This does not 'prove' that Organism 2 is the primary pathogen (as it could be an opportunistic, secondary invader), but by examining a reasonable number (in this case, 30) of cases and non-cases we are much better able understand the relative importance of the three organisms.}}
 === Planning a field epidemiological study ===

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 Epidemiologic studies can be broadly grouped into ''observational study, intervention study'' and ''theoretical epidemiology''.
-The characteristics of different study types are described briefly below and the advantages and disadvantages of each type are summarised. For more information on epidemiological study design, readers should consult standard epidemiology texts ([#_ENREF_17 Martin et al., 1987];[#_ENREF_23 Thrusfield, 1995];[#_ENREF_20 Rothman et al., 2008]; [#_ENREF_6 Dohoo et al., 2010]).
+The characteristics of different study types are described briefly below and the advantages and disadvantages of each type are summarised. For more information on epidemiological study design, readers should consult standard epidemiology texts ([#17 Martin et al., 1987];[#23 Thrusfield, 1995];[#20 Rothman et al., 2008]; [#6 Dohoo et al., 2010]).
 In disease investigations, almost all field studies will be observational studies.

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 N<sub>Cases</sub> = 20
-Number at risk = 1000 â€“ 0.5*400 â€“ 0.5*20 = 790
+Number at risk = 1000 - 0.5*400 - 0.5*20 = 790
 Cumulative incidence = 20/790 = 0.025 = 2.5%

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 With widespread access to the internet and library services, searching for information is now relatively easy. Most search engines search using keywords that you enter and searches may be conducted against the title or abstract of a paper, authors or the entire content.
-Searches can be refined by adding more terms and constructing logical search statements. Different search engines handle multiple terms differently, often using an â€˜advanced searchâ€™ page to set detailed search parameters. In PubMed and Medline, terms can be combined in a search statement using AND and OR logical operators. For example: â€˜dogs and hepatitisâ€™; â€˜â€johneâ€™s diseaseâ€ or paratuberculosisâ€™. If AND and OR operators are combined in one statement, the AND part will be processed first, then the OR, unless the OR is contained in parentheses.
+Searches can be refined by adding more terms and constructing logical search statements. Different search engines handle multiple terms differently, often using an 'advanced search' page to set detailed search parameters. In PubMed and Medline, terms can be combined in a search statement using AND and OR logical operators. For example: 'dogs and hepatitis'; '"johne's disease" or paratuberculosis'. If AND and OR operators are combined in one statement, the AND part will be processed first, then the OR, unless the OR is contained in parentheses.
 {{example|Example: [cattle and Johne's disease or paratuberculosis] is different to [cattle and (Johne's disease or paratuberculosis)]. The first statement will retrieve all resources for Johne's disease in cattle or paratuberculosis in any species, while the second returns only resources relating to Johne's disease in cattle or paratuberculosis in cattle. }}

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 ''1= endemic level, 2=ascending branch of epidemic, 3=peak of epidemic, 4=descending branch of epidemic, 5=secondary peak''.
-[[Image:Component of an epidemic curve.svg]]
+[[Image:Component of an epidemic curve.svg|500px|Centre|Components of an epidemic curve]]
 The slope of the ascending branch can indicate the type of exposure (propagating or common source) or the mode of transmission and incubation period of the disease agent. If transmission is rapid and the incubation period short, then the ascending branch will be steeper than if transmission is slow or if the incubation period is long.