ABSTRACT
Chlamydia abortus (C. abortus) infection and Q fever caused by Coxiella burnetii (C. brunetii) are zoonotic diseases caused by obligate intracellular bacteria. The infections cause economic losses in sheep and goat production systems in many parts of the world. The diseases are also of public health importance since they can infect humans. Information on the status of the two infections and risk factors responsible for the outbreak infections in sheep and goats is limited or lacking in Kenya, especially in pastoral communities. Moreover, molecular detection for confirming infections in shoats has not been exploited widely in Kenya. As a consequence, the objective of this study was to investigate into the presence of Q-fever and C. abortus infection in sheep and goats in five selected wards in Kajiado County. One hundred and thirty pastoralist flocks were selected from the five wards, which included Ildamat (27 flocks), Iloodokilani (27 flocks), Matapato south (25 flocks), Kenyawa-Poka (21 flocks), and Kaputiei north (30 flocks). After that, 1560 sheep and goat blood samples were collected from these flocks in the five wards. The samples were then transported to the Department of Public health, Pharmacology Laboratory for further analysis. The genomic DNA was extracted from whole blood samples using the Gene JET commercial Mini-Kit according to the manufacturer's instructions. Oligonucleotide primer targeting IS1111transposase element of C. brunetti and 16S-23S rRNA of C. abortus was used to amplify the DNAs by polymerase chain reaction (PCR) using the Veriti 96 well thermos-cycler. The amplicons were electrophoresed, stained, and visualized by a gel documentation imager. To assess the risk factors as well as to establish knowledge, attitudes, and practices of the pastoralist farmers, questionnaires were administered to respondents responsible for the flock. The prevalence of the two infections was estimated, and risk factors were determined by logistic regression. Coxiella burnetti-DNA was not detected in all samples analyzed. Chlamydia abortus DNA was detected in 86 (24.8%) sheep and goats blood samples, with 30(20.3%) samples being detected in sheep while 56 (28.1%) samples were detected in goats. Although samples positive for C. abortus-DNA were more in goats than those in sheep, the difference observed was not statistically significant (P <0.0.5). The prevalence of C. abortus in the five wards was 34.96% in Ildamat, 31.6% in Iloodokilani, 10.9% in Mathapato south 15.4% in Kenyawa poka, and 18.4% in Kaputiei. Approximately 56% of the farmers reported abortions as the main problem in their flocks. They believed that infections such as Brucellosis, Rift valley fever, tick-borne diseases were the major problems in their flocks. The study also found that 27.7% of the respondents were aware of zoonotic diseases. Furthermore, it was also observed that 39 (30%) farmers were aware that some of these diseases could also be transmitted to humans through the consumption of milk and meat. The risk factors associated with C. abortus infection were the watering points for animals during the wet season (OR=1.57, P=0.02), abortions (OR.84, P=0.02), and consumption of fermented raw milk by household pastoralists (OR=1.25, P= 0.05). In conclusion, it appears that sheep and goats raised in Kajiado County are infected with C. abortus. Transmission of C. abortus may be enhanced by overcrowding of sheep and goats at a drinking point during the wet season, as well as abortion in flocks. Further research on detection and risk factors of the two infections among pastoralists is recommended.
TABLE OF CONTENTS
DEDICATION: iv
ACKNOWLEDGEMENT v
TABLE OF CONTENTS vi
LIST OF TABLES xi
LIST OF FIGURES xii
LIST OFABBREVIATION: xiii
ABSTRACT: xv
CHAPTER ONE
INTRODUCTION
1.1. Background information: 2
1.2. Problem statement: 4
1.3. Justification: 5
1.4. Hypothesis of research: 6
1.5. Objectives: 6
1.5.1. General objective 6
1.5.2. Specific objectives 6
CHAPTER TWO
LITERATURE REVIEW
2.1 Etiology of Chlamydia abortus and Coxeilla burnetii 7
2.1.1 Etiology of Chlamydia abortus: 7
2.1.2 Etiology of Coxiella burnetii. 7
2.2 Epidemiology of Chlamydia abortus and Coxeilla buretii: 8
2.2.1. Epidemiology of Chlamydia abortus 8
2.2.2. Epidemiology of Coxiella burnetii 9
2.3 Lifecycle of Chlamydia abortus and Coxiella burnetii 9
2.3.1 Lifecycle of Chlamydia abortus. 9
2.3.2 Lifecycle of Coxiella burnetii. 11
2.4 Transmission of Chlamydia and Coxiella to human 13
2.4.1 Transmission of Chlamydia abortus to human: 13
2.4.2. Transmission of Coxiella burnetii to human: 13
2.5. Transmission of Chlamydia and Coxiella in animals. 14
2.5.1. Transmission of Chlamydia abortus in animals. 14
2.5.2. Transmission of Coxiella burnetii in animals. 14
2.6. Clinical signs of Chlamydia and Coxiella in human 15
2.6.1. Clinical signs of Chlamydia abortus in human. 15
2.6.2. Clinical signs of Coxiella burnetii in human. 15
2.7. Clinical signs of Chlamydia and Coxiella in animals 16
2.7.1. Clinical signs of Chlamydia abortus in animals 16
2.7.2. Clinical signs of Coxiella burnetii in animals. 16
2.8. Diagnosis of Chlamydia and Coxiella 17
2.8.1. Diagnosis of Chlamydia abortus 17
2.8.2. Diagnosis of Coxiella burnetii 18
2.9. Treatment of Chlamydia and Coxiella infections. 20
2.9.1. Treatment of Chlamydia abortus infection. 20
2.9.2. Treatment of Coxiella burnetii infection. 20
2.10. Control of Chlamydia and Coxiella infections 21
2.10.1. Control of Chlamydia abortus 21
2.10.2. Control of Coxiella burnetii 21
CHAPTER THREE
MATERIALS AND METHODS
3.1. Study area 22
3.2. Study design: 23
3.3. Target population: 23
3.4. Sample size determination: 23
3.5. Selection of the study participants: 24
3.6. Collection of blood samples: 25
3.7. Detection of Chlamydia abortus and Coxiella burnetti DNAs: 25
3.7.1. Extraction of DNA from the blood. 25
3.7.2 Amplification of Coxiella burnetti DNA by PCR 26
3.7.3 Amplification of Chlamydia abortus DNA by PCR 27
3.8. Questionnaire survey: 28
3.9. Data management and analysis. 28
3.9.1. Data management: 28
3.9.2. Data analysis: 28
3.10. Ethical approvals and considerations. 29
CHAPTER FOUR
RESULTS
4.1. Coxiella burnetii DNA detected in blood. 30
4.2. Chlamydia abortus DNA detected in blood. 31
4.3 Chlamydia abortus DNA detected in sheep and goats in the selected wards. 33
4.4. Small ruminant farmers’ demographic characteristics. 34
4.5. Farm management practices of pastoralists 37
4.6 Pastoralists reported reproduction challenges. 40
4.7. Contribution of Farmers’ practices to Public health risk. 41
4.8 Awareness of farmers on risk of zoonotic diseases. 43
4.9 Univariate risk analysis Result 44
4.10 Multivariate risk analysis result 44
CHAPTER FIVE
DISCUSSION
CHAPTER SIX
CONCLUSION AND RECOMMENDATION
6.1 Conclusion: 52
6.2. Recommendation: 53
REFERENCES 54
APPENDIX 1: Questionnaire and observational assessment for risk factors 64
APPENDIX 2: Consent form 70
APPENDIX 3: Guidelines for sampling of animals: 75
APPENDIX 4: Blood sampling data collection. 78
APPENDIX 5: Flock ID 80
LIST OF TABLES
Table 1: Number of sheep and goats blood samples tested for C. abortus and C. burnetii by PCR. 32
Table 2: Chlamydia abortus DNA detected in blood samples of the selected wards 33
Table 3: Proportion of sheep and goats testing positive for C. abortus DNA per ward 34
Table 4: Description of demographic information of the 130 respondents in Kajiado county. 36
Table 5: Results of farm management practices of pastoralists in Kajiado County Kenya 39
Table 6: Pastoralists reported reproductive challenges in their flocks (sheep and goats) in Kajiado county Kenya (n=130) 40
Table 7: Contribution of practices of farmers to public health risks 42
Table 8: Analysis of awareness with regards to zoonotic diseases among the farmers (n=130). 43
Table 9: Univariate analysis of Chlamydia abortus outcome variable among 130 sheep and goats’ farms in Kajaido, county Kenya 45
Table 10: Multivariate logistic model for variable associated with Chlamydia abortus molecular positivity for 130 sheep and goat farms, Kajaido county Kenya 46
LIST OF FIGURES
Figure 1: Lifecycle of C. abortus showing the different stages of the bacterium during the 6-8days of the lifecycle. 10
Figure 2: Lifecycle of C. burnetii showing the different stages of the bacterium during the 14 days of the lifecycle 12
Figure 3: A map of Kajiado County, Kenya highlighting the various wards in the County… 22
Figure 4: Blank Gel-image of representative samples analyzed by conventional PCR. The absence of band indicated failure to detect C. burnetii DNA. 30
Figure 5: Gel-image of representative samples analyzed by conventional PCR for C. abortus . 31 1-10 samples are representative of the samples analyzed. 31
LIST OFABBREVIATION
BBSRC - Biotechnology and biological sciences research council
BLAST - Basic local alignment search tool
bp - Base pair
C. abortus - Chlamydia abortus
C. burnetii - Coxiella burnetii
CFT - Complement fixation test
DNA - Deoxyribonucleic acid
dNTP - Deoxynucleotide triphosphate
EB - Elementary body
OIE - Organization for Animal Health
OR - Odd’s ratio
PCR - Polymerase chain reaction
PHPT - Public Health Pharmacology and Toxicology
SPSS - Statistical Package for Social Sciences
RNA - Ribonucleic acid
RB - Reticulate body
WB1 - Wash buffer 1
WB 2 - Wash buffer 2
CHAPTER ONE
INTRODUCTION
1.1. Background information
Chlamydia abortus (C. abortus) infection and Q fever caused by Coxiella burnetii (C. brunetii) are important obligate intracellular bacterial infections of livestock and humans that cause clinical conditions resulting in infertility and production loss. The diseases are clinically and epidemiologically significant worldwide, both in humans and animals (Rohde et al., 2010). Chlamydia abortus is a gram-negative, intracellular obligate bacterium that infects sheep and goats' mucosa (Cheong et al., 2019). Chlamydia is distributed throughout the world, causing various diseases in both humans and animals (Szymańska-Czerwińska et al., 2017). Chlamydia abortus is zoonotic disease. Although most human infections are mild and often unnoticed, pregnant women can develop severe, life threatening illnesses and abortions (Nietfeld, 2001).
Chlamydia abortus is transmitted through aborted products such as fetus and placenta. The other mode of transmission includes oral route and inhalation of dust particles by the susceptible animals (Bagley, 2001). In many countries, it is one of the causes of abortion and fetal loss in sheep and goats (Li et al., 2015). Subsequently, the disease causes a significant negative impact on the livestock industry in many countries worldwide (Cheong et al., 2019). Chlamydia abortus infection causes serious economic losses in both animal production performance and public health. The cost is as result of high prevalence of the disease and high costs of diagnosis, vaccination, treatment, and management (Postma et al, 2002).
Q-fever is a bacterial infection that causes a variety of clinical symptoms in livestock, including infertility and production loss (Njeru et al., 2016). All domesticated ruminants are susceptible with the cases of reproductive failures such as abortions, stillbirths, and infertility being reported.
Typically, Q-fever infection is asymptomatic, and the animals can remain infected for a long time without showing clinical signs (Scolamacchia et al., 2010). Infection in humans usually occurs via inhalation of contaminated aerosols (Klemmer et al., 2018). Q-fever usually manifests as nonspecific symptoms such as high fever of up to 410C, severe headache, fatigue, chills, cough nausea, vomiting and diarrhea. These nonspecific symptoms can progress to severe chronic disease and in most cases they can be misdiagnosed (Scolamacchia et al., 2010). The economic and public health impacts of Q fever remain a major concern in developing countries because Q fever causes significant loss of animal productivity (Tagesu, 2019). The disease causes heavy economic losses in flocks due to abortions and birth of weak offspring (Eibach et al., 2012).
Due to abortions and the birth of weak offspring, the disease causes significant economic losses to pastoralists. Nevertheless, in some situations, the animals can recover without complications (Eibach et al., 2012). Coxiella burnetii infection, can last for years, and domestic ruminants are often subclinical carriers, the hosts can shed the bacteria in various excretions such as urine, milk, faeces, placental and birth fluids (Abbas et al., 2011). A seroprevalence of 54.2% for C. burnetii has been reported for goats reared in the Somali and Oromia regional states of southern Ethiopia (Tagesu, 2019). In Kenya, the seroprevalence of C. burnetii in sheep and goats has been reported to be 57.5% and 83.1% respectively (Njeru et al., 2016) .
Detection of Q-fever and C. abortus infections in sheep and goats is critical for effective control of the two diseases (Barkallah, et al., 2018). Subsequently, some studies have documented the use of molecular techniques such as PCR for the detection of the two pathogens. Other studies have also focused on detection of circulating antibodies in order to assess the level of exposure to the bacterial infection (Jung et al., 2014). The most effective way to reduce the impact of these pathogen infections on flock health and productivity is to improve the ability to monitor and avoid pathogen transmission. Therefore, small ruminant management and environmental factors that increase the risk of infection must be taken into account. In this regard, it has been also possible to assess the risk factors associated with outbreaks of Q-fever and C. abortus infections in sheep and goats (Talafha et al. 2009). These risk factors include awareness of farmers, abortions, raising the flocks in crowded conditions among others (Merdja et al., 2015). In this study, C. abortus and
C. brunetii were detected by molecular analysis using PCR. The risk factors responsible for the outbreaks of the two diseases were also assessed in Kajiado County in Kenya.
1.2. Problem statement
Chlamydia abortus is one of the most common causes of reproductive losses in sheep and goats globally, except in Australia and New Zealand, which are disease-free. In many sheep-rearing areas worldwide, Chlamydial abortion in late pregnancy causes major economic loss, mainly where flocks are densely concentrated during the kidding and lambing season (Longbottom, 2008). Being zoonotic disease, C. abortus is also a public health priority disease (Selim, 2016). In Kenya, an antibody against C. abortus has been previously detected in sea sheep (Wandera, J. G. et al., 1971). In addition, the state of abortions and reproductive defects in livestock, such as premature birth, death and weak offspring, have been linked to Q fever. Q fever is a serious zoonosis because it is extremely infectious in humans and can be a risk to veterinarians, laboratory employees and abattoir workers (Anderson et al., 2013). A recent serological study has revealed that the overall prevalence of Q fever in sheep and goats in Kajiado is 57.5% and 83.1%, respectively (Njeru et al., 2016).
Chlamydia abortus and Coxiella burnetii are known to infect sheep and goats in many regions of the world except in Australia and New Zealand. The current information on the infections of sheep and goats with the two pathogens is either limited or lacking in Kenya. Furthermore, molecular detection of C. abortus and C. burnetii infecting sheep and goats in Kenya has never been exploited yet. This detection technique could be useful in confirmation of active infections. There is also a lack of updated information on the risk factors responsible for the outbreak for the two infections. Therefore, this study determined the concurrence and associated risk factors of Chlamydia infection and Q-fever in sheep and goats in select areas in Kajiado County, Kenya.
1.3. Justification
Livestock plays an essential role in the livelihood of the majority of population in Kajaido County. Pastoralism is a significant economic activity in the County, with the crucial stocks being cattle, sheep, and goats. Small ruminants are ranked high in importance since they are a source of regular cash income and insurance against tragedies. Chlamydia abortus and Coxiella burnetii are the most common infectious causes of abortion and the birth of weak lambs in many small ruminant- rearing countries. The abortions are common in the last two to three weeks of pregnancy (Barati et al., 2017). These infections are under-reported and under-diagnosed, mainly because the symptoms are mostly non-specific, making diagnosis difficult (Anderson et al., 2013).
Therefore, this research has focused on the identification of C. abortus and C. burnetii from sheep and goats in Kajaido County in Kenya. Subsequently, this study has provided preliminary data on molecular identification of C. abortus and C. burnetii and the risk factors responsible the transmission and outbreaks of Q-fever and C. abortus infection. In this regard, the information generated here can assist with strategies for controlling and preventing the infections in animals and humans. If these diseases are controlled and prevented, then the production losses associated with outbreaks of the two diseases will be minimized. This will eventually ensure increased production of sheep and goats thereby enhancing food security, improving public health and livelihoods among pastoralists community.
1.4. Hypothesis of research
• Sheep and goats reared in Kajiado County are not infected with C. abortus and C. burnetii.
• There are no risk factors associated with C.abortus and C. burnetii infections in small ruminants in Kajiado County.
1.5. Objectives:
1.5.1. General objective:
To assess the occurrence and evaluate risk factors of C. abortus and C. burnetii infection in small ruminants in Kajiado
1.5.2. Specific objectives:
1. To identify C. burnetii and C. abortus infecting sheep and goats in selected areas in Kajiado County, Kenya.
2. To analyze risk factors associated with C. abortus and C. burnetii infections in sheep and goats in Kajaido County, Kenya
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