Difference between revisions of "Salmonella meleagridis: Dose Response Models"

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==<center>'''''Salmonella enterica'' serotype Meleagridis'''</center>==
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==<center>'''''Salmonella meleagridis'''''</center>==
  
 
<center><big>'''Author: Sushil Tamrakar'''</big></center>
 
<center><big>'''Author: Sushil Tamrakar'''</big></center>
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==='''General overview of ''Salmonella'' and Salmonellosis'''===
 
==='''General overview of ''Salmonella'' and Salmonellosis'''===
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''Salmonella'' is a genus of rod-shaped, gram-negative, non-spore forming, predominantly motile enterobacteria (Chalker and Blaser 1988). Many species of ''Salmonella'' have been isolated from eggs and egg products (McCullough and Eisele 1951). ''Salmonella meleagridis'' is one of the most common serotype of ''Salmonella'' (Zaidi, McDermott et al. 2006). Twenty human isolates of ''S. meleagridis'' had been identified in Canada so far during 1997.
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http://www.cdc.gov/salmonella/
  
''Salmonella'' is a genus of rod-shaped, gram-negative, non-spore forming, predominantly motile enterobacteria, that cause more than 10<sup>4</sup> cases of infections per year in the United States. Salmonellosis is an important medical problem; although infection with non-typhoid ''Salmonella'' often causes mild self-limited illness, severe sequelae including death may occur, particularly in immunocompromised hosts. The incidence of salmonellosis is higher in developing than in developed countries and in developing countries, food handlers may be a reservoir for further transmission of infection. ref name="Chalker and Blaser 1988">
 
Chalker RB, Blaser MJ (1988) [http://www.jstor.org/stable/4454281 A review of human salmonellosis: III. Magnitude of Salmonella infection in the United States.] Reviews of Infectious Diseases 10(1): 111-124.</ref>
 
  
Many species of ''Salmonella'' have been isolated from eggs and egg products. <ref name="McCullough and Eisele 1951,1">McCullough NB, Eisele CW (1951) Experimental Human Salmonellosis: III. Pathogenicity of Strains of Salmonella newport, Salmonella derby, and Salmonella bareilly Obtained from Spray-Dried Whole Egg. The Journal of Infectious Diseases 89(3): 209-213.</ref>. ''Salmonella enterica'' serotype Meleagridis is one of the most common serotypes of Salmonella. <ref name="Zaidi, McDermott et al. 2006">Zaidi MB, McDermott PF, et al. (2006) Nontyphoidal Salmonella from Human Clinical Cases, Asymptomatic Children, and Raw Retail Meats in Yucatan, Mexico. Clinical Infectious Diseases 42(1): 21-28.</ref>. Twenty human isolates of ''S. Meleagridis'' had been identified in Canada so far during 1997.
 
  
 
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{{DRSummaryTableNonpreferredModel|expID= 240 |refer=McCullough and Eisele 1951,2|reference=McCullough NB, Eisele CW (1951) Experimental human salmonellosis. II. Immunity studies following experimental illness with Salmonella meleagridis and Salmonella anatum. Journal of immunology (Baltimore, Md. : 1950) 66(5): 595-608.|host= human |agentStrain= strain III |route= oral, with eggnog |nDoses= 4 |doseUnits= CFU|response= infection |bestFitModel=beta-Poisson|parameters=&alpha; =  8.85E-01 , N<sub>50</sub> =  5.24E+05|N50= 5.24E+05 }}
 
{{DRSummaryTableNonpreferredModel|expID= 240 |refer=McCullough and Eisele 1951,2|reference=McCullough NB, Eisele CW (1951) Experimental human salmonellosis. II. Immunity studies following experimental illness with Salmonella meleagridis and Salmonella anatum. Journal of immunology (Baltimore, Md. : 1950) 66(5): 595-608.|host= human |agentStrain= strain III |route= oral, with eggnog |nDoses= 4 |doseUnits= CFU|response= infection |bestFitModel=beta-Poisson|parameters=&alpha; =  8.85E-01 , N<sub>50</sub> =  5.24E+05|N50= 5.24E+05 }}
 
{{DRSummaryTableEnd}}
 
{{DRSummaryTableEnd}}
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==<sup>*</sup>Recommended Model==
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Eexperiment number 238 is the recommended one as the strain I was more virulent than strain III.
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[[File:Exponential and betapoisson model.jpg|thumb|none|550px]]
 
[[File:Exponential and betapoisson model.jpg|thumb|none|550px]]
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==='''Optimization Output for experiment 238'''===
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==='''Optimization Output for experiment 238 (''Salmonella meleagridis'')'''===
  
{{DRExperimentDataTable11|title=Human / ''Salmonella'' Meleagridis strain I data|refer = McCullough and Eisele 1951,2|reference=McCullough NB, Eisele CW (1951) Experimental human salmonellosis. II. Immunity studies following experimental illness with Salmonella meleagridis and Salmonella anatum. Journal of immunology (Baltimore, Md. : 1950) 66(5): 595-608.|pos=Infected|neg=Non-infected |d1=12000|p1=3|n1=3|t1=6|d2=24000|p2=4|n2=2|t2=6|d3=52000|p3=3|n3=3|t3=6|d4=96000|p4=3|n4=3|t4=6|d5=155000|p5=5|n5=1|t5=6|d6=3E+05|p6=6|n6=0|t6=6|d7=720000|p7=4|n7=1|t7=5|d8=1150000|p8=6|n8=0|t8=6|d9=5.5E+06|p9=5|n9=1|t9=6|d10=2.4E+07|p10=5|n10=0|t10=5|d11=5E+07|p11=6|n11=0|t11=6}}
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{{DRExperimentDataTable11|title=Human / ''S. meleagridis'' strain I data|refer = McCullough and Eisele 1951,2|reference=McCullough NB, Eisele CW (1951) Experimental human salmonellosis. II. Immunity studies following experimental illness with Salmonella meleagridis and Salmonella anatum. Journal of immunology (Baltimore, Md. : 1950) 66(5): 595-608.|pos=Infected|neg=Non-infected |d1=12000|p1=3|n1=3|t1=6|d2=24000|p2=4|n2=2|t2=6|d3=52000|p3=3|n3=3|t3=6|d4=96000|p4=3|n4=3|t4=6|d5=155000|p5=5|n5=1|t5=6|d6=3E+05|p6=6|n6=0|t6=6|d7=720000|p7=4|n7=1|t7=5|d8=1150000|p8=6|n8=0|t8=6|d9=5.5E+06|p9=5|n9=1|t9=6|d10=2.4E+07|p10=5|n10=0|t10=5|d11=5E+07|p11=6|n11=0|t11=6}}
  
  
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==='''Optimization Output for experiment 240'''===
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==='''Optimization Output for experiment 240 (''Salmonella meleagridis'')'''===
  
{{DRExperimentDataTable4|title=Human/ Salmonella meleagridis strain III data|refer = McCullough and Eisele 1951,2|reference=McCullough NB, Eisele CW (1951) Experimental human salmonellosis. II. Immunity studies following experimental illness with Salmonella meleagridis and Salmonella anatum. Journal of immunology (Baltimore, Md. : 1950) 66(5): 595-608.|pos=Infected|neg=Non-infected |d1=158000|p1=1|n1=5|t1=6|d2=1.5E+06|p2=5|n2=1|t2=6|d3=7680000|p3=6|n3=0|t3=6|d4=1E+07|p4=5|n4=1|t4=6}}
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{{DRExperimentDataTable4|title=Human/ ''S. meleagridis'' strain III data|refer = McCullough and Eisele 1951,2|reference=McCullough NB, Eisele CW (1951) Experimental human salmonellosis. II. Immunity studies following experimental illness with Salmonella meleagridis and Salmonella anatum. Journal of immunology (Baltimore, Md. : 1950) 66(5): 595-608.|pos=Infected|neg=Non-infected |d1=158000|p1=1|n1=5|t1=6|d2=1.5E+06|p2=5|n2=1|t2=6|d3=7680000|p3=6|n3=0|t3=6|d4=1E+07|p4=5|n4=1|t4=6}}
  
  
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[[File:BPscatter ID240.png|thumb|left|500px|'''Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.''']][[File:BPmodel ID240.png|thumb|none|500px|'''beta Poisson model plot, with confidence bounds around optimized model''']]<br>
 
[[File:BPscatter ID240.png|thumb|left|500px|'''Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.''']][[File:BPmodel ID240.png|thumb|none|500px|'''beta Poisson model plot, with confidence bounds around optimized model''']]<br>
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==='''Summary'''===
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==='''References'''===
  
The data set of ''Salmonella'' Meleagridis strain II failed to show test of trend and hence was not analyzed. Strain II and strain III could not be pooled.
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<references />
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Chalker RB and Blaser MJ (1988) A Review of Human Salmonellosis: III. Magnitude of ''Salmonella'' Infection in the United States. ''Reviews of Infectious Diseases'' 10(1), 111-124.
  
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McCullough NB and Eisele CW (1951) Experimental Human Salmonellosis: II. Immunity Studies Following Experimental Illness with ''Salmonella Meleagridis'' and ''Salmonella Anatum''. ''The Journal of Immunology'' 66(5), 595-608.
  
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McCullough NB and Eisele CW (1951) Experimental Human Salmonellosis: III. Pathogenicity of Strains of ''Salmonella newport'', ''Salmonella derby'', and ''Salmonella bareilly'' Obtained from Spray-Dried Whole Egg. ''The Journal of Infectious Diseases'' 89(3), 209-213.
  
==='''References'''===
+
Zaidi MB, McDermott PF, Fedorka-Cray P, Leon V, Canche C, Hubert SK, Abbott J, León M, Zhao S, Headrick M and Tollefson L (2006) Nontyphoidal ''Salmonella'' from Human Clinical Cases, Asymptomatic Children, and Raw Retail Meats in Yucatan, Mexico. ''Clinical Infectious Diseases'' 42(1), 21-28.
 
 
<references />
 
  
  
  
 
[[Category:Completed Dose Response Models: Bacteria]][[Category:Dose Response Model]][[Category:Salmonella (Meleagridis)]]
 
[[Category:Completed Dose Response Models: Bacteria]][[Category:Dose Response Model]][[Category:Salmonella (Meleagridis)]]

Latest revision as of 20:04, 20 November 2013

Salmonella meleagridis

Author: Sushil Tamrakar


General overview of Salmonella and Salmonellosis

Salmonella is a genus of rod-shaped, gram-negative, non-spore forming, predominantly motile enterobacteria (Chalker and Blaser 1988). Many species of Salmonella have been isolated from eggs and egg products (McCullough and Eisele 1951). Salmonella meleagridis is one of the most common serotype of Salmonella (Zaidi, McDermott et al. 2006). Twenty human isolates of S. meleagridis had been identified in Canada so far during 1997.


http://www.cdc.gov/salmonella/



Summary Data

McCullough, and Eisele (1951) inoculated human volunteers orally with the S. Meleagridis strain I,II and III.[1]


Experiment serial number Reference Host type Agent strain Route # of doses Dose units Response Best fit model Optimized parameter(s) LD50/ID50
238* [1] human strain I oral, with eggnog 11 CFU infection beta-Poisson α= 3.89E-01 , N50 = 1.68E+04 1.68E+04
240 [1] human strain III oral, with eggnog 4 CFU infection beta-Poisson α = 8.85E-01 , N50 = 5.24E+05 5.24E+05
*This model is preferred in most circumstances. However, consider all available models to decide which one is most appropriate for your analysis.


*Recommended Model

Eexperiment number 238 is the recommended one as the strain I was more virulent than strain III.


Exponential and betapoisson model.jpg



Optimization Output for experiment 238 (Salmonella meleagridis)

Human / S. meleagridis strain I data [1]
Dose Infected Non-infected Total
12000 3 3 6
24000 4 2 6
52000 3 3 6
96000 3 3 6
155000 5 1 6
3E+05 6 0 6
720000 4 1 5
1150000 6 0 6
5.5E+06 5 1 6
2.4E+07 5 0 5
5E+07 6 0 6


Goodness of fit and model selection
Model Deviance Δ Degrees
of freedom
χ20.95,1
p-value
χ20.95,m-k
p-value
Exponential 71.8 63.8 10 3.84
1.33e-15
18.3
1.98e-11
Beta Poisson 7.99 9 16.9
0.535
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.


Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 3.89E-01 1.23E-01 1.74E-01 2.01E-01 1.12E+00 1.91E+00 3.82E+02
N50 1.68E+04 7.98E+01 1.08E+03 2.27E+03 4.78E+04 5.71E+04 7.49E+04


Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.
beta Poisson model plot, with confidence bounds around optimized model


Optimization Output for experiment 240 (Salmonella meleagridis)

Human/ S. meleagridis strain III data [1]
Dose Infected Non-infected Total
158000 1 5 6
1.5E+06 5 1 6
7680000 6 0 6
1E+07 5 1 6


Goodness of fit and model selection
Model Deviance Δ Degrees
of freedom
χ20.95,1
p-value
χ20.95,m-k
p-value
Exponential 7.81 5.51 3 3.84
0.019
7.81
0.0501
Beta Poisson 2.3 2 5.99
0.316
Beta-Poisson fits better than exponential; cannot reject good fit for beta-Poisson.


Optimized parameters for the beta-Poisson model, from 10000 bootstrap iterations
Parameter MLE estimate Percentiles
0.5% 2.5% 5% 95% 97.5% 99.5%
α 8.85E-01 1.78E-01 2.91E-01 3.68E-01 1.40E+03 1.71E+03 8.24E+03
N50 5.24E+05 4.71E+04 1.20E+05 1.92E+05 1.19E+06 1.39E+06 1.90E+06


Parameter scatter plot for beta Poisson model ellipses signify the 0.9, 0.95 and 0.99 confidence of the parameters.
beta Poisson model plot, with confidence bounds around optimized model



References

  1. 1.0 1.1 1.2 1.3 1.4 McCullough NB, Eisele CW (1951) Experimental human salmonellosis. II. Immunity studies following experimental illness with Salmonella meleagridis and Salmonella anatum. Journal of immunology (Baltimore, Md. : 1950) 66(5): 595-608.

Chalker RB and Blaser MJ (1988) A Review of Human Salmonellosis: III. Magnitude of Salmonella Infection in the United States. Reviews of Infectious Diseases 10(1), 111-124.

McCullough NB and Eisele CW (1951) Experimental Human Salmonellosis: II. Immunity Studies Following Experimental Illness with Salmonella Meleagridis and Salmonella Anatum. The Journal of Immunology 66(5), 595-608.

McCullough NB and Eisele CW (1951) Experimental Human Salmonellosis: III. Pathogenicity of Strains of Salmonella newport, Salmonella derby, and Salmonella bareilly Obtained from Spray-Dried Whole Egg. The Journal of Infectious Diseases 89(3), 209-213.

Zaidi MB, McDermott PF, Fedorka-Cray P, Leon V, Canche C, Hubert SK, Abbott J, León M, Zhao S, Headrick M and Tollefson L (2006) Nontyphoidal Salmonella from Human Clinical Cases, Asymptomatic Children, and Raw Retail Meats in Yucatan, Mexico. Clinical Infectious Diseases 42(1), 21-28.