Presentation by Martin Wainaina, Johanna F. Lindahl, Ian Dohoo, Anne Mayer-Scholl, Kristina Roesel, Deborah Mbotha, Uwe Roesler, Delia Grace, Bernard Bett and Sascha Al Dahouk at the 16th International Symposium of Veterinary Epidemiology and Economics, Halifax, Canada, 11 August 2022.

1. ISVEE16 – Halifax, Canada
16th International Symposium of Veterinary
Epidemiology and Economics (ISVEE 16)
Connecting Animals, People, and their shared
environments
Longitudinal study of small ruminant zoonoses in
Tana River, Kenya
Martin Wainaina 1,2,3, *, Johanna F. Lindahl 3,4,5, Ian Dohoo 6, Anne Mayer-Scholl 1, Kristina Roesel 2,3, Deborah Mbotha 2,3, Uwe Roesler 7,
Delia Grace 3,8, Bernard Bett 3 and Sascha Al Dahouk 1,9
1. German Federal Institute for Risk Assessment; 2. Department of Veterinary Medicine, Freie Universität Berlin; 3. International Livestock Research Institute; 4. Uppsala University;
5. Swedish University of Agricultural Sciences; 6. University of Prince Edward Island; 7. Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin;
8. Natural Resources Institute, University of Greenwich; 9. RWTH Aachen University Hospital
22nd International Symposium of Veterinary Epidemiology and Economics
Halifax, Canada, 11 August 2022

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Introduction
Wainaina et al., PLoS Neg. Trop. Dis., 2022
• Many infectious diseases causing febrile disease in Africa
• Major problem with diagnostic capabilities
• Many of them zoonotic

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Introduction
0
0.02
0.04
0.06
0.08
0.1
0.12
0.14
0.16
0.18
0.2
% patients
Top 50 fever agents in Eastern Africa
Wainaina et al., PLoS Neg. Trop. Dis., 2022

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Environmental
changes
Climate changes
Direct effects on
vector capacity
More precipitation gives more breeding
grounds.
Increased hatching of desiccated eggs.
Higher temperature gives shorter
extrinsic incubation periods.
Shorter mosquito life cycles.
Mosquitoes more susceptible to
infection.
Effects on host
availability
Droughts make more
intense concentrations of
livestock and wildlife at
waterholes.
Less vegetation force
pastoralists to herd longer
distances and get further
into forest or riverine
areas.
Land-use
changes
Effects on
vectors
Irrigation and dams
provide breeding
habitats
Effects on hosts
Increased livestock
densities.
Reduced biodiversity
reduces the dilution
effect of non-host
animals.
More farmed land moves
pastoralists to less
suitable areas.
Changes & disease

5. ISVEE16 – Halifax, Canada
FAO STATS, 2022
Land-use changes
More and more range lands in Africa are
being converted to crop lands through
irrigation to alleviate food insecurity
Results: major trade-offs in ecosystem
services
• More food produced (provisioning
services) at the expense of biodiversity
and regulatory services (disease,
flooding, erosion)
0.1
0.2
0.3
0.4
0.5
1960 1980 2000 2020
year
percent
Agricultural land equipped for irrigation

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FAO STATS, 2022
Changes in livestock production
Kenya is experiencing
increases in both goat
and sheep production
Sheep
Fresh whole milk production (tonnes)
Sheep
Meat production (tonnes)
Goat
Fresh whole milk production (tonnes)
Goat
Meat production (tonnes)
1960 1980 2000 2020 1960 1980 2000 2020
20000
40000
60000
80000
20000
40000
60000
80000
1e+05
2e+05
20000
40000
60000
year
value

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What is prioritized?
Munyua et al., PLoS One, 2015
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1 Normalized Final Scores
Decreasing priority rank

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What is being studied in Kenya?
0
10
20
1960 1980 2000 2020
Year
Count
Agent
Brucella
Coxiella
Leptospira
PubMed search hits of
Brucella/Leptospira/Coxiella AND
Kenya

9. ISVEE16 – Halifax, Canada
Moreno, Front. Microbiol., 2014; Atluri, Annu. Rev. Microbiol., 2011
Brucellosis

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Ko et al., Nat. Rev. Microbiol., 2019
Leptospirosis

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Cutler, Lancet Infect. Dis., 2002
Q-fever (coxiellosis)
Caused by Coxiella burnetii

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Objectives
Estimating seroprevalence and incidence rates in small ruminants in Kenya
• Survey methods that consider sampling weights and multistage nature of
sampling.
Identifying risk factors for seropositivity and seroconversion
• Also with survey weighting.
• Seasonal variations of seroconversions.

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Tana
River
County
Indian
Ocean
Somalia
Ethiopia
South
Sudan
Uganda
Tanzania
Wikipedia
Study area

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Initial cross-sectional study
• 3 sites (8 villages) –
purposive
• 37 households – random
• 316 small ruminants –
random
• 228 (72.2%) goats
• 88 (27.9%) sheep
•
Longitudinal study
• 247 animals followed up
• 55 were lost to follow-up
• Replaced by 69 animals
6 visits
Mbotha, Transbound. Emerg. Dis., 2017
Data collected
• Animal data
age, sex, species,
herd size,
reproductive status,
site, household
Study design

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Whole blood/
Serum
Leptospira
spp.
Whole
blood
LipL32
qPCR
Serum
MAT testing
Brucella
spp.
Serum
Parallel
IS711 and
bcsp31
qPCR
Parallel
RBT and
IgG ELISA.
CFT
confirmation
Coxiella
burnetii
Serum
IS1111
qPCR
IgG ELISA
Lab testing

16. ISVEE16 – Halifax, Canada
• Results from first samples of animals only
• Estimates adjusted for the complex survey design
• Sample weights - inverse probability weights
Total weights=
Total households
Households sampled
∗
Total small ruminants
Small ruminants sampled
• Multi-stage sampling
Animal → Household → Village (PSUs) → Sites
• Analysis on R environment. Survey package version 4.0
Data analysis - seroprevalence

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• Results from first samples of animals only.
• All variables intervening when site is main
exposure variable.
• Complex survey design: sampling weights
and multistage sampling
• Co-exposure model for the three zoonoses.
SI: Site; S: Sex; A/S: Age/Sex; HS: Herd size;
RS: Reproductive Status; Z: Seropositivity
Data analysis – Risk factors

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• Survey-weighted Poisson regression models.
• Risk factors for seroconversions – not done because of few
seroconversions per primary sampling unit
Data analysis – Seroconversions

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Weighted seroprevalence
Category Variable Positives Total % (95% CI) SE
Coxiella burnetii
Total 66 316 34.6 (24.3–47.0) 4.7
Site
Irrigated 34 139 24.1 (7.9–54.0) 9.3
Pastoral 25 69 38.7 (17.4–65.0) 8.2
Riverine 7 108 4.4 (1.87–10.0) 1.7
Leptospira spp.
Total † 48 313 15.3 (11.6–20.0) 1.7
Site
Irrigated 15 138 17.2 (6.8–37.0) 5.8
Pastoral 8 68 13.9 (5.3–32.0) 4.0
Riverine 25 107 26.9 (15.5–42.0) 6.2
Brucella spp.
Total 4 316 - -
Site
Irrigated 3 139 - -
Pastoral 0 69 - -
Riverine 1 108 - -
† Three animals removed from analyses (doubtful MAT results and lost to follow-up)

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Odds Ratio
Agent Variable Estimate Lower 95% CI Upper 95% CI SE p-Value
Coxiella burnetii Riverine Ref.
Irrigated 6.83 2.58 18.06 0.50 0.01
Pastoral 13.61 13.61 13.61 0.00 0.00
Observations = 316; Pseudo-R² (McFadden) = 0.05
Leptospira spp. Irrigated Ref.
Pastoral 0.78 0.36 1.70 0.40 0.56
Riverine 1.77 0.81 3.88 0.40 0.21
Observations = 313 †; Pseudo-R² (McFadden) = 0.01
† Three animals removed from analyses (doubtful MAT results and lost to follow-up)
Total effect of site

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Dependant variable Independent variables † Odds ratio 95% CI SE p-Value
Leptospira spp. Coxiella burnetii 2.52 2.29-2.77 0.05 0.00
Brucella spp. 1.52 0.06-41.23 1.68 0.82
Coxiella burnetii Leptospira spp. 2.51 2.28-2.77 0.05 0.00
Brucella spp. 3.62 0.27-48.91 1.33 0.40
Brucella spp. Coxiella burnetii 3.80 0.40-36.08 1.15 0.33
Leptospira spp. 1.56 0.05-52.28 1.79 0.82
† All three survey-weighted models included site as well
Co-exposure to zoonoses

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Incidence per 100 animal-
months at risk
95% Confidence Intervals
Leptospira spp. Overall 1.8 1.3–2.5
Goat 1.8 1.2–2.6
Sheep 1.8 1.4–2.4
Coxiella burnetii Overall 1.3 0.7–2.3
Goat 1.3 0.7–2.3
Sheep 1.3 0.6–3.1
Brucella spp. Overall 0 -
Goat - -
Sheep - -
Serological incidence rates

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Seroconversions with time

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[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE] [CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
[CELLRANGE]
32
33
34
35
36
37
38
39
40
41
Sep 2014 Oct 2014 Nov 2014 Dec 2014 Jan 2015 Feb 2015 Mar 2015 Jun 2015
Quantification cycle
(Cq) value
Months with no Cq values were negative
Animal 102 (Brucella spp.)
Animal 115 (Brucella spp.)
Animal 370 (Brucella spp.)
Animal 48 (Brucella spp.)
Animal 75 (C. burnetii)
PCR detection
Labels “pos” and “neg” represent serology results

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0
5
10
15
20
25
30
35
Number of animals positive at first sampling
Leptospiral serovars

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Leptospiral serovars
Changes in agglutinating serovars in
animals (n=11)

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Irrigation and pastoralism are risk factors for spread of coxiellosis.
Control (e.g. vaccination, properly composting manure, rodent control) is
needed.
Co-exposure to multiple pathogens. Need for integrated disease
surveillance and control.
Need for systematic disease prioritization of animal diseases in Kenya.
Conclusions

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Link to full open-access publication → https://doi.org/10.3390/microorganisms10081546

29. THANK YOU