| Literature DB >> 25979286 |
Thomas M Lietman1, Teshome Gebre2, Amza Abdou3, Wondu Alemayehu4, Paul Emerson2, Seth Blumberg5, Jeremy D Keenan6, Travis C Porco7.
Abstract
Mathematical models predict that the prevalence of infection in different communities where an infectious disease is disappearing should approach a geometric distribution. Trachoma programs offer an opportunity to test this hypothesis, as the World Health Organization (WHO) has targeted trachoma to be eliminated as a public health concern by the year 2020. We assess the distribution of the community prevalence of childhood ocular chlamydia infection from periodic, cross-sectional surveys in two areas of Ethiopia. These surveys were taken in a controlled setting, where infection was documented to be disappearing over time. For both sets of surveys, the geometric distribution had the most parsimonious fit of the distributions tested, and goodness-of-fit testing was consistent with the prevalence of each community being drawn from a geometric distribution. When infection is disappearing, the single sufficient parameter describing a geometric distribution captures much of the distributional information found from examining every community. The relatively heavy tail of the geometric suggests that the presence of an occasional high-prevalence community is to be expected, and does not necessarily reflect a transmission hot spot or program failure. A single cross-sectional survey can reveal which direction a program is heading. A geometric distribution of the prevalence of infection across communities may be an encouraging sign, consistent with a disease on its way to eradication.Entities:
Keywords: Eradication; Geometric distribution; Mass drug administration; Trachoma; Transmission model
Mesh:
Substances:
Year: 2015 PMID: 25979286 PMCID: PMC4986606 DOI: 10.1016/j.epidem.2015.03.003
Source DB: PubMed Journal: Epidemics ISSN: 1878-0067 Impact factor: 4.396
Model fitting for individual visits of TANA, ranked by AICc of models for that visit. The best-fit shape and scale parameters are included.
| Visit | AICc | Distribution | Parameters | logLikelihood | Shape | Scale |
|---|---|---|---|---|---|---|
| TANA baseline | 173.55 | Negative Binomial | 5 | –80.107 | 8.352 | 0.395 |
| 187.12 | Discrete Weibull | 5 | –86.894 | 1.345 | 1.000 | |
| 190.30 | Poisson | 4 | –90.097 | 0.397 | ||
| 193.53 | Zero-inflated Poisson | 5 | –90.097 | 0.397 | 0.000 | |
| 193.72 | Geometric | 4 | –91.809 | 0.395 | ||
| 196.95 | Zero-inflated Geometric | 5 | –91.809 | 0.395 | 0.000 | |
| 218.73 | Binomial | 4 | –104.314 | 0.397 | ||
| TANA 18 months | 105.21 | Geometric | 4 | –47.551 | 0.043 | |
| 108.16 | Discrete Weibull | 5 | –47.411 | 1.101 | 0.051 | |
| 108.19 | Negative Binomial | 5 | –47.429 | 1.270 | 0.043 | |
| 108.44 | Zero-inflated Geometric | 5 | –47.551 | 0.043 | 0.000 | |
| 117.63 | Zero-inflated Poisson | 5 | –52.150 | 0.054 | 0.204 | |
| 120.70 | Poisson | 4 | –55.297 | 0.043 | ||
| 122.78 | Binomial | 4 | –56.338 | 0.043 | ||
| TANA 24 months | 96.71 | Geometric | 4 | –43.304 | 0.036 | |
| 99.48 | Zero-inflated Poisson | 5 | –43.071 | 0.053 | 0.327 | |
| 99.84 | Discrete Weibull | 5 | –43.256 | 1.066 | 0.040 | |
| 99.87 | Negative Binomial | 5 | –43.270 | 1.160 | 0.036 | |
| 99.91 | Zero-inflated Geometric | 5 | –43.287 | 0.037 | 0.034 | |
| 106.46 | Poisson | 4 | –48.179 | 0.036 | ||
| 107.53 | Binomial | 4 | –48.711 | 0.036 | ||
| TANA 30 months | 67.88 | Geometric | 4 | –28.885 | 0.015 | |
| 69.92 | Zero-inflated Poisson | 5 | –28.294 | 0.032 | 0.529 | |
| 70.40 | Zero-inflated Geometric | 5 | –28.532 | 0.020 | 0.257 | |
| 70.66 | Negative Binomial | 5 | –28.663 | 0.590 | 0.015 | |
| 70.72 | Discrete Weibull | 5 | –28.695 | 0.855 | 0.013 | |
| 73.47 | Poisson | 4 | –31.681 | 0.015 | ||
| 73.80 | 4 | –31.847 | 0.015 | |||
| TANA 36 months | 85.71 | Geometric | 4 | –37.804 | 0.026 | |
| 88.33 | Zero-inflated Geometric | 5 | –37.499 | 0.032 | 0.173 | |
| 88.39 | Discrete Weibull | 5 | –37.530 | 0.853 | 0.021 | |
| 88.41 | Negative Binomial | 5 | –37.539 | 0.655 | 0.026 | |
| 90.82 | Zero-inflated Poisson | 5 | –38.745 | 0.047 | 0.440 | |
| 99.13 | Poisson | 4 | –44.511 | 0.027 | ||
| 100.16 | Binomial | 4 | –45.028 | 0.027 |
Fig. 1(a) Distribution of the prevalence of ocular chlamydia infection in 1-5 year-old children in 24 communities in the TEF study, Gurage, Ethiopia. (Lakew et al., 2009a) Communities were treated biannually with mass oral azithromycin. The distribution of infection for each cross-sectional survey is displayed as a density plot, in which each community’s contribution is the Bayesian posterior derived from the observed prevalence and a non-informative, uniform prior. The prevalence clearly decreases from baseline (black curve) to post-treatment visits at 12, 18, and 24 months (progressively lighter grey curves). (b) Distribution of the prevalence of ocular chlamydia infection in 0–9 year-old children in 24 communities in the TANA study, Amhara, Ethiopia. (Gebre et al., 2012) Communities were treated annually or biannually. The prevalence decreases from baseline (black curve) to post-treatment visits at 18, 24, 30, and 36 months (progressively lighter grey curves).
Model fitting for individual visits of simulated SIS model, ranked by AICc of models for that visit. The best-fit shape and scale parameters are included. Parameters for the model include: population of 50 children per community, R0 = 2.6 (in the absence of treatment), estimated R = 1.0 (in the presence of treatment)(Melese et al., 2004), 80% coverage with 100% effective antibiotic, rate of recovery 1/52 weeks.
| Visit | AICc | Distribution | Parameters | Log Likelihood | Shape | Scale |
|---|---|---|---|---|---|---|
| Simulated baseline | 148.55 | Poisson | 1 | −73.183 | 0.395 | |
| 150.94 | Zero-inflated Poisson | 2 | −73.183 | 0.572 | 1.000 | |
| 150.94 | Negative Binomial | 2 | −73.183 | 1120,000 | 0.397 | |
| 159.10 | Binomial | 1 | −78.462 | 0.000 | ||
| 206.20 | Discrete Weibull | 2 | −100.814 | 1.223 | 0.395 | |
| 212.02 | Geometric | 1 | −104.917 | 0.000 | ||
| 214.41 | Zero-inflated Geometric | 2 | −104.917 | 0.573 | 0.397 | |
| Simulated 18 months | 151.41 | Negative Binomial | 2 | −73.419 | 4.261 | 0.043 |
| 151.66 | Discrete Weibull | 2 | −73.546 | 1.669 | 0.051 | |
| 160.52 | Zero-inflated Poisson | 2 | −77.972 | 0.197 | 0.043 | |
| 160.49 | Geometric | 1 | −79.152 | 0.000 | ||
| 162.87 | Zero-inflated Geometric | 2 | −79.152 | 0.189 | 0.204 | |
| 169.14 | Poisson | 1 | −83.477 | 0.043 | ||
| 179.79 | Binomial | 1 | −88.804 | 0.043 | ||
| Simulated 24 months | 165.43 | Negative Binomial | 2 | −80.429 | 3.944 | 0.036 |
| 167.17 | Discrete Weibull | 2 | −81.297 | 1.506 | 0.327 | |
| 174.50 | Geometric | 1 | −86.161 | 0.040 | ||
| 176.89 | Zero-inflated Geometric | 2 | −86.161 | 0.257 | 0.036 | |
| 182.11 | Zero-inflated Poisson | 2 | −88.769 | 0.268 | 0.034 | |
| 197.62 | Poisson | 1 | −97.720 | 0.036 | ||
| 222.16 | Binomial | 1 | −109.989 | 0.036 | ||
| Simulated 30 months | 174.68 | Negative Binomial | 2 | −85.053 | 4.651 | 0.015 |
| 179.35 | Discrete Weibull | 2 | −87.390 | 1.401 | 0.529 | |
| 185.06 | Zero-inflated Poisson | 2 | −90.243 | 0.345 | 0.257 | |
| 186.29 | Geometric | 1 | −92.052 | 0.015 | ||
| 188.68 | Zero-inflated Geometric | 2 | −92.052 | 0.331 | 0.013 | |
| 208.15 | Poisson | 1 | −102.983 | 0.015 | ||
| 241.48 | Binomial | 1 | −119.651 | 0.015 | ||
| Simulated 36 months | 111.89 | Discrete Weibull | 2 | −53.662 | 1.802 | 0.026 |
| 112.17 | Negative Binomial | 2 | −53.799 | 5.766 | 0.173 | |
| 112.64 | Zero-inflated Poisson | 2 | −54.033 | 0.078 | 0.021 | |
| 112.64 | Poisson | 1 | −55.229 | 0.026 | ||
| 113.73 | Binomial | 1 | −55.775 | 0.440 | ||
| 118.57 | Geometric | 1 | −58.193 | 0.027 | ||
| 120.96 | Zero-inflated Geometric | 2 | −58.193 | 0.073 | 0.027 |
Model fit of the distribution of the community-level prevalence of infection in Ethiopian trachoma studies.
| TEF 12, 18, and 24 months | Shape parameter | No. of parameters | Loge Likelihood | AICc |
|---|---|---|---|---|
| 4 | −125.79 | 263.576 | ||
| 0.824 (0.364 to 1.663) | 5 | −125.58 | 265.165 | |
| 0.742 (0.335 to 1.526) | 5 | −125.76 | 265.528 | |
| 0.999 (0.750 to 1.289) | 5 | −125.79 | 265.580 | |
| 0.956 (0.934 to 0.972) | 5 | −130.91 | 275.815 | |
| 4 | −153.42 | 318.838 | ||
| 4 | −157.68 | 327.356 | ||
| 5 | −157.544 | 329.089 | ||
| 0.926 (0.674 to 1.412) | 6 | −157.435 | 330.871 | |
| 0.960 (0.462 to 1.820) | 6 | −157.535 | 331.070 | |
| 0.957 (0.935 to 0.976) | 6 | −157.894 | 331.788 | |
| 1.030 (0.792 to 1.363) | 6 | −158.390 | 332.779 | |
| 5 | −179.668 | 373.335 | ||
| 5 | −181.924 | 377.849 |
Prevalence of ocular chlamydial infection in longitudinal studies of trachoma in Ethiopia.
| Prevalence of Infection
| ||||
|---|---|---|---|---|
| Communities | Mean prevalence | Standard deviation of prevalence | Geometric distribution goodness of fit test
( | |
| TEF Ethiopia | ||||
| 0 Months | 16 | 0.529 | 0.218 | 0.03 |
| 12 Months | 16 | 0.069 | 0.109 | 0.23 |
| 18 Months | 16 | 0.032 | 0.037 | 0.58 |
| 24 Months | 16 | 0.020 | 0.022 | 0.30 |
| TANA Ethiopia | ||||
| 0 Months | 24 | 0.394 | 0.153 | 0.03 |
| 18 Months | 24 | 0.043 | 0.050 | 0.29 |
| 24 Months | 24 | 0.036 | 0.041 | 0.12 |
| 30 Months | 24 | 0.015 | 0.025 | 0.89 |
| 36 Months | 24 | 0.026 | 0.037 | 0.74 |