Case burden of waterborne microbes

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Question

What are the case burdens (in DALYs) of waterborne microbes? Case burden is the disease burden that is caused by one case of infection of a particular microbe. Infection may be latent or symptomatic, and it may or may not lead to more severe complications or even death.

Rationale

Data

The case burdens are presented as DALYs per infected individual. These include both those who get ill with the disease as well as those carrying the pathogen.

Case burdens of waterborne microbes(DALY/infection)

Obs	Response	Illness	Subgroup	Result	Description
1	giardia infection	gastroenteritis	Age:age 0-4	0.002425
2	giardia infection	gastroenteritis	Age:age 5-9	0.002732
3	giardia infection	gastroenteritis	Age:age 10-14	0.004313
4	giardia infection	gastroenteritis	Age:age 15-64	0.002572
5	giardia infection	gastroenteritis	Age:age 65-79	0.006245
6	giardia infection	gastroenteritis	Age:age 80+	0.006245
7	cryptosporidium infection	gastroenteritis	Age:age 0-4	0.001713
8	cryptosporidium infection	gastroenteritis	Age:age 5-9	0.002801
9	cryptosporidium infection	gastroenteritis	Age:age 10-14	0.004052
10	cryptosporidium infection	gastroenteritis	Age:age 15-64	0.001153
11	cryptosporidium infection	gastroenteritis	Age:age 65-79	0.001654
12	cryptosporidium infection	gastroenteritis	Age:age 80+	0.001654
13	cryptosporidium infection	death	Age:age 0-4	0.00056	probability of death of cryptosporidium infection 9.95E-07 in 0-4-year-olds
14	cryptosporidium infection	death	Age:age 5-9	0	probability of death of cryptosporidium infection 0 in 5-14-year-olds
15	cryptosporidium infection	death	Age:age 10-14	0	probability of death of cryptosporidium infection 0 in 5-14-year-olds
16	cryptosporidium infection	death	Age:age 15-64	0.000616	probability of death of cryptosporidium infection 2.09E-05 in 15-64-year-olds
17	cryptosporidium infection	death	Age:age 65-79	0.009315	probability of death of cryptosporidium infection 0.00164 in 65-81-year-olds
18	cryptosporidium infection	death	Age:age 80+	0.009315	probability of death of cryptosporidium infection 0.00164 in 65-81-year-olds
19	norovirus infection	gastroenteritis	Age:age 0-4	0.000692
20	norovirus infection	gastroenteritis	Age:age 5-9	0.000527
21	norovirus infection	gastroenteritis	Age:age 10-14	0.000558
22	norovirus infection	gastroenteritis	Age:age 15-64	0.000550
23	norovirus infection	gastroenteritis	Age:age 65-81	0.000516
24	norovirus infection	gastroenteritis	Age:age 80+	0.000516
25	norovirus infection	death	Age:age 0-4	0.000163	probability of death from norovirus 2.94E-06 in 0-4-year-olds
26	norovirus infection	death	Age:age 5-9	0	probability of death from norovirus 0 in 5-65-year-olds
27	norovirus infection	death	Age:age 10-14	0	probability of death from norovirus 0 in 5-65-year-olds
28	norovirus infection	death	Age:age 15-64	0	probability of death from norovirus 0 in 5-65-year-olds
29	norovirus infection	death	Age:age 65-79	0.00126	probability of death from norovirus 0.00024 in 66-81-year-olds
30	norovirus infection	death	Age:age 80+	0.00126	probability of death from norovirus 0.00024 in 66-81-year-olds
31	rotavirus infection	gastroenteritis	Age:age 0-4	0.001917
32	rotavirus infection	gastroenteritis	Age:age 5-9	0.001096
33	rotavirus infection	gastroenteritis	Age:age 10-14	0.001121
34	rotavirus infection	gastroenteritis	Age:age 15-64	0.000889
35	rotavirus infection	gastroenteritis	Age:age 65-81	0.000991
36	rotavirus infection	gastroenteritis	Age:age 80+	0.000991
37	rotavirus infection	death	Age:age 0-4	0.001514	probability of death from rotavirus is 2.13E-05 for 0-4-year-olds
38	rotavirus infection	death	Age:age 5-9	0	probability of death from rotavirus is 0 for people 5 years or older
39	rotavirus infection	death	Age:age 10-14	0	probability of death from rotavirus is 0 for people 5 years or older
40	rotavirus infection	death	Age:age 15-64	0	probability of death from rotavirus is 0 for people 5 years or older
41	rotavirus infection	death	Age:age 65-81	0	probability of death from rotavirus is 0 for people 5 years or older
42	rotavirus infection	death	Age:age 80+	0	probability of death from rotavirus is 0 for people 5 years or older
43	campylobacter infection	gastroenteritis		0.000973
44	campylobacter infection	clinical Guillian-Barré syndrome		0.000019	Probability of getting GBS if ill from campylobacter is 0.0002. DALY/case for clinical GBS is 0.29.
45	campylobacter infection	residual Guillian Barré syndrome		0.000383	Probability of getting GBS if ill from campylobacter is 0.0002. DALY/case for clinical GBS is 5.8
46	campylobacter infection	reactive arthritis		0.0001599	Probability of reactive arthritis if ill from campylobacter is 0.02, duration of illness 6 weeks, severity 2.1
47	campylobacter infection	death		0.001740	Probability of death from gastroenteritis is 0.0004, life lost 13.2 years. Probability of death from GBS is 0.02667, life lost 18.7 years.
48	E. coli infection	gastroenteritis		0.000273	Probability of gastroenteritis if ill from E. coli is 0.53, severity 0.067, duration 3.4 days.
49	E. coli infection	hemorrhagic colitis		0.002319	Probability of HC if ill from E. coli is 0.47, severity 0.39, duration 5.6 days.
50	E. coli infection	haemolytic uraemic syndrome		0.000441	Probability of HUS if ill from E. coli is 0.01, severity 0.93, duration 21 days.
51	E. coli infection	end stage renal disease		0.008466	Probability of ESRD if already with HUS is 0.118, DALY/case is 8.7.
52	E. coli infection	death		0.007231	Probability of death from E. coli infection is 0.00027, life lost 13.2 years. Probability of death from HUS is 0.04, life lost 26.2 years. Probability of death from ESRD is 0.0252, life lost 34 years.

Probability of illness, given infection(probability)

Obs	Response	Result
1	giardia infection	1
2	cryptosporidium infection	0.71
3	norovirus infection	0.7
4	rotavirus infection	0.9
5	campylobacter infection	0.33
6	E. coli infection	0.82

Data for Giardia used in the calculations. The probability of illness if infected is 1.

Treatment	Age	Probability of needing the treatment if ill	Duration (days)	Severity
untreated	0-4	0.9375	10	0.067
untreated	5-9	0.91034	10	0.067
untreated	10-14	0.72642	10	0.067
untreated	15-64	0.92486	10	0.067
untreated	65-81	0.5365	10	0.067
general practitioner	0-4	0.0609	10	0.393
general practitioner	5-9	0.0852	10	0.393
general practitioner	10-14	0.272	10	0.393
general practitioner	15-64	0.0721	10	0.393
general practitioner	65-81	0.451	10	0.393
hospitalised	0-4	0.0015	30	0.393
hospitalised	5-9	0.00446	30	0.393
hospitalised	10-14	0.00158	30	0.393
hospitalised	15-64	0.00304	30	0.393
hospitalised	65-81	0.0125	30	0.393

Data for Cryptosporidium used in the calculations. The probability of illness if infected is 0.71.

Treatment	Age	Probability of needing the treatment if ill	Duration (days)	Severity
untreated	0-4	0.91757	3.5	0.067
untreated	5-9	0.80937	3.5	0.067
untreated	10-14	0.68105	3.5	0.067
untreated	15-64	0.97742	3.5	0.067
untreated	65-81	0.94706	3.5	0.067
general practitioner	0-4	0.082	7	0.393
general practitioner	5-9	0.188	7	0.393
general practitioner	10-14	0.316	7	0.393
general practitioner	15-64	0.0209	7	0.393
general practitioner	65-81	0.0367	7	0.393
hospitalised	0-4	0.00043	18.4	0.393
hospitalised	5-9	0.00263	18.4	0.393
hospitalised	10-14	0.0029	18.4	0.393
hospitalised	15-64	0.00166	18.4	0.393
hospitalised	65-81	0.0146	18.4	0.393

Data for norovirus used in the calculations. The probability of illness if infected is 0.7.

Treatment	Age	Probability of needing the treatment if ill	Duration (days)	Severity
untreated	0-4	0.94877	3.8	0.067
untreated	5-9	0.9902	3.8	0.067
untreated	10-14	0.98239	3.8	0.067
untreated	15-65	0.98434	3.8	0.067
untreated	66-81	0.992741	3.8	0.067
general practitioner	0-4	0.0448	5.73	0.393
general practitioner	5-9	0.0086	5.73	0.393
general practitioner	10-14	0.0154	5.73	0.393
general practitioner	15-65	0.0137	5.73	0.393
general practitioner	66-81	0.00617	5.73	0.393
hospitalized	0-4	0.00643	7.23	0.393
hospitalized	5-9	0.0012	7.23	0.393
hospitalized	10-14	0.00221	7.23	0.393
hospitalized	15-65	0.00196	7.23	0.393
hospitalized	66-81	0.00089	7.23	0.393

The data for rotavirus used in the calculations. The probability of illness if infected is 0.9.

Treatment	Age	Probability of needing the treatment if ill	Duration (days)	Severity
untreated	0-4	0.82	4.9	0.067
untreated	5-14	0.95	4.9	0.067
untreated	15-64	0.99	4.9	0.067
untreated	65-81	0.97	4.9	0.067
general practitioner	0-4	0.137	7.1	0.393
general practitioner	5-9	0.0244	7.1	0.393
general practitioner	11-14	0.0511	7.1	0.393
general practitioner	15-64	0.0127	7.1	0.393
general practitioner	65-81	0.0299	7.1	0.393
hospitalized	0-4	0.0416	7.7	0.393
hospitalized	5-9	0.0213	7.7	0.393
hospitalized	10-81	0	7.7	0.393

The data for gastroenteritis cases caused by a campylobacter infection used in the calculations. The probability of illness if infected is 0.33, and the probability of the illness being gastroenteritis is 0.98.----arg8024: . I assume it's 0.98, since the probability of arthritis is 0.02 and the the probability of gbs is 0.0002. --Heta (talk) 13:31, 3 July 2019 (UTC) (type: truth; paradigms: science: comment)

Treatment	Probability of needing the treatment if ill	Duration (days)	Severity
untreated	0.7627	5.1	0.067
general practitioner	0.2373	8.4	0.393
hospitalized	0.0097	14.2	0.393

Calculations

+ Show code- Hide code # This is code "Op_en7947/caseburden" on page [[Case burden of waterborne microbes]]. library(OpasnetUtils) case_burden <- Ovariable("case_burden", ddata="Op_en7947", subset="Case burdens of waterborne microbes") objects.latest("Op_en2031", code_name="subgrouping") # [[ERF]] subgrouping case_burden@data <- subgrouping(case_burden@data) objects.store(case_burden) cat("Ovariable case_burden saved. \n")

+ Show code- Hide code # This is code "Op_en7947/caseburden_ilness" on page [[Case burden of waterborne microbes]]. library(OpasnetUtils) probability <- Ovariable("probability", ddata="Op_en7947", subset="Probability of illness, given infection") case_burden_illness <- Ovariable( "case_burden_illness", dependencies= data.frame( Name=c("probability", "case_burden"), Ident=c(NA, "Op_en7947/caseburden") ), formula=function (...) { return(case_burden/probability) } ) objects.store(case_burden_illness) cat("Ovariable case_burden_illness saved. \n")

See also

• Vesiopas (in Finnish)
• Water guide