Systematic review of causes and factors associated with morbidity and mortality on smallholder dairy farms in eastern and southern Africa

Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review

Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.

Calf morbidity, mortality, and management practices in dairy farms in Jimma City, Southwestern Ethiopia

BACKGROUND

This research aims to determine the incidence of calf morbidity, mortality and its potential predisposing factors in the first six months of life. Morbidity and mortality of dairy calves are persistent problems for dairy farmers worldwide. For effective control and prevention programs on calf health, it is imperative to estimate the extent of calf morbidity and mortality, and associated risk factors. Although few studies have investigated the epidemiology of calf morbidity and mortality in Ethiopia, comprehensive information is scarce in this area.

METHODS

Data were collected through a cross-sectional survey and longitudinal follow-up on purposively selected dairy farms. A longitudinal study was conducted on 235 calves from birth to 6 months of age. Survival analysis methods using the Kaplan-Meier (K-M) method, and mixed effect Cox proportional hazard regression were employed to compute the life-to-event data on morbidity and mortality.

RESULTS

From the 235 calves studied, 53 morbidity and 15 mortality events were recorded. This gives an overall morbidity and mortality incidence rate of 55 per 100-calf 6-months at risk (risk rate of 42.07%) and 14 per 100-calf 6-months at risk (risk rate of 12.97%), respectively. Diarrhea (13.84%) followed by pneumonia (8.97%) were the most common diseases that occurred in calves, respectively. Similarly, diarrhea (33.3%) and pneumonia (26.7%) were the leading causes of death. Dam parity (p < 0.001) and pen cleaning (p < 0.001) were significant predictors of calf morbidity. Dam parity (p = 0.007), calving status (p = 0.005), pen cleaning (p = 0.04), and floor type (p = 0.001) of houses were significantly associated with mortality. The hazard of diarrhea was significantly associated with sex (p = 0.003), first colostrum feeding time (p = 0.028), pen cleaning (p = 0.010), and breeding method (p = 0.013).

CONCLUSION

The rates of morbidity and mortality reported in the study were higher than the economically acceptable, also affecting the welfare of the animals. The risk factors found need due attention in the management practices of dairy calves in Ethiopia.

Longitudinal study of calf morbidity and mortality and the associated risk factors on urban and peri-urban dairy farms in southern Ethiopia

BACKGROUND

Calf morbidity and mortality are among the leading causes of economic losses on dairy farms around the world. Poor calf management practices exacerbate the problem in developing countries like Ethiopia. This prospective, longitudinal study was conducted on 70 selected dairy farms in southern Ethiopia with the aim of estimating calf morbidity and mortality rates, identifying the associated risk factors and determining whether the mortality rate is above economically tolerable levels. For this purpose, a total of 274 calves on 70 farms were followed up every two weeks from birth to six months of age for major clinical health problems and deaths.

RESULTS

The study found a morbidity rate of 13.2 cases and a mortality rate of 3.8 cases per 100 calf-months at risk in the study calves. The cumulative incidence of morbidity and mortality was also found to be 40.29% and 12.85%, respectively. Diarrhea was the leading cause of morbidity and mortality in calves, accounting for 71.3% and 62.1% of all morbidity and mortality, respectively. In a multivariable Cox regression analysis, the risk of morbidity was significantly (p = 0.022) higher in calves born to dystocia-affected dams (HR = 2.4) and on farms where dairy farming is the farmers' secondary source of income (HR = 1.7). However, the risk of morbidity was significantly (p < 0.001) lower in calves older than three months (HR = 0.22), female calves (HR = 0.57), calves raised by farmers who had completed secondary school (HR = 0.26) or college education (HR = 0.30). Similarly, calves aged over three months (HR = 0.14), calves separated from their dams only after ingestion of colostrum (HR = 0.40) and calves owned by farmers who completed secondary school (HR = 0.08) or college education (HR = 0.13) all had lower mortality rates than other groups. On the other hand, calves born to cows with dystocia were 5.2 times more likely to die.

CONCLUSION

The study concluded that calf morbidity and mortality rates in the study area are higher than economically tolerable levels and therefore it is recommended to raise awareness among farmers to improve calf management practices.

Incidence of morbidity and mortality in calves from birth to six months of age and associated risk factors on dairy farms in Hawassa city, southern Ethiopia

Calf morbidity and mortality are major causes of economic losses on dairy farms worldwide, with a far greater impact in developing countries such as Ethiopia. A prospective longitudinal study on dairy farms in the city of Hawassa was conducted between August 2018 and July 2019, to estimate the cumulative incidence of calf morbidity and mortality and to identify the associated risk factors. For this purpose, 221 calves from 20 farms were examined every 15 days from birth to the age of six months. We used the Kaplan Meier (K-M) method, log rank test, and Cox proportional hazards regression to analyze the data. Of the calves examined, 48.4% (n = 107) had various clinically visible health problems, while 19.5% (n = 43) died from various causes. Using the K-M method, the cumulative incidence of all-cause morbidity at the end of the sixth month of life was 50.12% (95% CI: 43.58%–57.05%), while the cumulative incidence of all-cause mortality was 20.04% (95% CI: 12.56%–26.06%). The most commonly diagnosed disease syndrome was diarrhea (64.5%), followed by pneumonia (15%), septicemia (6.5%), joint disease (4.7%), conjunctivitis (3.7%), umbilical infections (2, 8%) and other unknown causes (11.2%). Diarrhea was also the leading cause of death (46.5%). The other causes of calf mortality were pneumonia (16.3%), septicemia (7%), and unknown diseases (30.2%). In the K-M hazard analysis, the greatest risk of calf morbidity and mortality was observed during the first month of life and then the risk decreased significantly as the calves grew. Of the 21 potential risk factors studied, the multivariable Cox proportional hazards regression model showed that time calves ingested their first colostrum, calving difficulty, and calving season were the three predictors that were significantly associated with a higher risk of morbidity and mortality. A higher risk of morbidity was observed in calves that had ingested their first colostrum six hours after birth (HR = 1.9; P = 0.003), had calving difficulties (HR = 2.96; P < 0.001) and were born in the rainy season (HR = 1.64; P = 0.017) compared to calves that had consumed colostrum immediately after birth, had no difficulties at birth and were born in the dry season. The same three factors have been identified to influence calf mortality. The mortality risk was 2.73 (P = 0.002), 4.62 (P < 0.001) and 2.74 (P = 0.002) times higher in calves that had difficulty calving, ingested their first colostrum meal six hours after birth and were born in the rainy season, respectively. In general, the calf morbidity and mortality rates identified in this study were beyond economically justifiable limits and calls for educating farmers to raise awareness of some easy-to-fix issues such as colostrum feeding.

Moving towards sustainable breeding objectives and cow welfare in dairy production: a South African perspective

Genetic advancements have resulted in improved dairy production over many decades, due to the focus of breeding objectives on production as the driving force for genetic progress and overall farm profitability. Major advancements were made in the easy-to-measure traits with moderate to high heritability, which resulted in unintended consequences on herd fertility, health, and welfare of cows. In addition, climate change and animal welfare concerns demanded balanced breeding objectives and selection approaches for sustainable production-including health and longevity. The inclusion of genomic information into genetic evaluations has been proved to benefit traits associated with welfare and sustainable production. Cow welfare traits remain complex and suitable phenotypes are not always easy to measure or readily available for genetic evaluations. The challenge for improvement of cow welfare often lies within implementation of sensitive and measurable parameters. The aim of this review was to explore the reconsideration of breeding objectives in the dairy industry towards sustainable dairy production and cow welfare with reference to selection of dairy animals in South Africa.

Isolation and characterization of E. coli strains causing intramammary infections from dairy animals and wild birds

The study was conducted to estimate the prevalence of Escherichia coli (E. coli) in sub-clinically mastitic (SCM) animals, and in wild and migratory birds which may act as reservoir disseminating such pathogen. Farm hygiene, management and milking procedures were listed through a questionnaire. Thirty lactating cows and 15 lactating buffaloes from five small-scale dairy farms were randomly selected and screened for subclinical mastitis (SCM) using California Mastitis Test (CMT) and somatic cell count (SCC). In addition, 80 teat skin swabs, 5 drinking water samples and 38 wild and migratory bird faecal matter were also collected. All samples were processed for E. coli isolation by culturing on Levine’s Eosin Methylene Blue (L-EMB) agar, followed by purification and biochemical identification. Positive samples were subjected to molecular identification and serotyping. In addition, the presence of extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing E. coli have been reported by antimicrobial sensitivity testing. Escherichia coli were isolated from 7.7%, 50% and 50% of the positive CMT cows’ quarters, cows’ composite and buffaloes’ composite milk samples, respectively. In addition, 14% of cows’ teats, 20% of water samples, 70% of faecal matter from wild bird, and 33.3% of faecal matter from migratory waterfowls were carrying E. coli. Serotyping, antibiotic-resistant pattern and phylogenetic analysis have pointed the bearable implication of milking hygiene and wild birds in disseminating E. coli strains causing intramammary infections.

Knowledge and risk factors for foot-and-mouth disease among small-scale dairy farmers in an endemic setting

Foot-and-mouth disease (FMD) is a highly contagious viral infection of cloven-hoofed animals. In Kenya, the disease is endemic with outbreaks typically occurring throughout the year. A cross-sectional study was undertaken in Nakuru County to investigate farmer knowledge and risk factors for clinical disease. Semi-structured interviews were conducted on 220 smallholder farmers, selected using random spatial sampling. The majority of respondents (207/220 [94.1%]) knew of FMD and 166/207 (80.2%) of them could correctly identify the disease based on their knowledge of the clinical signs. Forty-five out of 220 farmers (20.4%) vaccinated their livestock against FMD in the previous 6 months, although of those who knew of FMD only 96/207 (46.4%) perceived it as a preventive measure undertaken to reduce the risk of disease in their farm. FMD had occurred in 5.9% of the surveyed farms within the previous 6 months (from May to November 2016). Using multivariate analysis, the use of a shared bull (OR = 9.7; p = 0.014) and the number of sheep owned (for each additional sheep owned OR = 1.1; p = 0.066) were associated with an increased likelihood of a farm experiencing a case of FMD in the previous 6 months, although the evidence for the latter was weak. This study reports risk factors associated with clinical FMD at the farm level in a densely populated smallholder farming area of Kenya. These results can be used to inform the development of risk-based strategic plans for FMD control and as a baseline for evaluating interventions and control strategies.

Aspects of lameness in pasture based dairy systems

Pasture-based dairy systems are implemented all over the world. Access to pasture is perceived to be advantageous for animal welfare in western societies. However, the benefits of grazing on lameness are not uniformly verifiable. This is related to the challenges that grazing cows face which are different from zero-grazing systems to some extent, but may nevertheless be deleterious. The distribution of lesion types comparing housed and pastured cattle differs between studies. This may be caused by differences in how strongly certain risk factors apply in these studies. Major risk factors for lameness in grazing cattle are related to the risk of trauma, for example from long walking distances and lack of track maintenance, and cow factors such as the adaptability of certain breeds to the grazing lifestyle. The consequences of lameness are similar to zero-grazing cattle and negatively affect animal welfare and productivity.

Distribution of ticks infesting ruminants and risk factors associated with high tick prevalence in livestock farms in the semi-arid and arid agro-ecological zones of Pakistan

Background

Tick infestation is the major problem for animal health that causes substantial economic losses, particularly in tropical and subtropical countries. To better understand the spatial distribution of tick species and risk factors associated with tick prevalence in livestock in Pakistan, ticks were counted and collected from 471 animals, including 179 cattle, 194 buffaloes, 80 goats and 18 sheep, on 108 livestock farms in nine districts, covering both semi-arid and arid agro-ecological zones.

Results

In total, 3,807 ticks representing four species were collected: Hyalomma anatolicum (n = 3,021), Rhipicephalus microplus (n = 715), Hyalomma dromedarii (n = 41) and Rhipicephalus turanicus (n = 30). The latter species is reported for the first time from the study area. Rhipicephalus microplus was the predominant species in the semi-arid zone, whereas H. anatolicum was the most abundant species in the arid zone. The overall proportion of tick-infested ruminants was 78.3% (369/471). It was highest in cattle (89.9%), followed by buffaloes (81.4%), goats (60.0%) and sheep (11.1%). The median tick burden significantly differed among animal species and was highest in cattle (median 58), followed by buffaloes (median 38), goats (median 19) and sheep (median 4.5). Female animals had significantly higher tick burdens than males and, in large ruminants, older animals carried more ticks than younger animals. The intensity of infestation was significantly lower in indigenous animals compared to exotic and crossbred cows. Analysis of questionnaire data revealed that the absence of rural poultry, not using any acaricides, traditional rural housing systems and grazing were potential risk factors associated with a higher tick prevalence in livestock farms.

Conclusion

Absence of rural poultry, not performing acaricide treatments, traditional rural housing systems and grazing were important risk factors associated with higher tick prevalence in livestock farms. Age, gender, breed and animal species significantly affected the intensity of tick infestation. This report also describes the presence of R. turanicus in the Punjab Province of Pakistan for the first time. The outcomes of this study will be useful in the planning of integrated control strategies for ticks and tick-borne diseases in Pakistan.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-017-2138-0) contains supplementary material, which is available to authorized users.

Improving dairy production in Malawi: a literature review

Milk production in Malawi is stagnating while steadily increasing in neighboring countries. We performed a literature review to identify factors negatively affecting milk production in Malawi and propose potential solutions to overcome the particular constraints. We structured the analysis along the value chain with three major components: upstream providers, on-farm production, and downstream providers. It is shown that the literature strongly focuses on on-farm constraints and most prominently on animal health, breed choice, and milk yield. The literature research did not reveal any reasons specific to Malawi that would hinder an increase in milk production as experienced in neighboring countries. We suggest a focus on crossbreeds accompanied by local breeding programs, which would reduce dependence on imported semen and strengthen the currently unreliable artificial insemination services. In addition, crossbreeds may be better suited than pure breeds for current feeding practices and climate conditions and thus come close to reaching their genetic potential. We conclude that cost advantages of crossbreeds clearly compensate for the lower revenues compared with exotic breeds such as Holstein-Friesian or Jersey.

Impact of foot-and-mouth disease on mastitis and culling on a large-scale dairy farm in Kenya

Foot and mouth disease (FMD) is a highly transmissible viral infection of cloven hooved animals associated with severe economic losses when introduced into FMD-free countries. Information on the impact of the disease in FMDV-endemic countries is poorly characterised yet essential for the prioritisation of scarce resources for disease control programmes. A FMD (virus serotype SAT2) outbreak on a large-scale dairy farm in Nakuru County, Kenya provided an opportunity to evaluate the impact of FMD on clinical mastitis and culling rate. A cohort approach followed animals over a 12-month period after the commencement of the outbreak. For culling, all animals were included; for mastitis, those over 18 months of age. FMD was recorded in 400/644 cattle over a 29-day period. During the follow-up period 76 animals were culled or died whilst in the over 18 month old cohort 63 developed clinical mastitis. Hazard ratios (HR) were generated using Cox regression accounting for non-proportional hazards by inclusion of time-varying effects. Univariable analysis showed FMD cases were culled sooner but there was no effect on clinical mastitis. After adjusting for possible confounders and inclusion of time-varying effects there was weak evidence to support an effect of FMD on culling (HR = 1.7, 95% confidence intervals [CI] 0.88-3.1, P = 0.12). For mastitis, there was stronger evidence of an increased rate in the first month after the onset of the outbreak (HR = 2.9, 95%CI 0.97-8.9, P = 0.057).

Mortality in East African shorthorn zebu cattle under one year: predictors of infectious-disease mortality

BACKGROUND

Infectious livestock diseases remain a major threat to attaining food security and are a source of economic and livelihood losses for people dependent on livestock for their livelihood. Knowledge of the vital infectious diseases that account for the majority of deaths is crucial in determining disease control strategies and in the allocation of limited funds available for disease control. Here we have estimated the mortality rates in zebu cattle raised in a smallholder mixed farming system during their first year of life, identified the periods of increased risk of death and the risk factors for calf mortality, and through analysis of post-mortem data, determined the aetiologies of calf mortality in this population. A longitudinal cohort study of 548 zebu cattle was conducted between 2007 and 2010. Each calf was followed during its first year of life or until lost from the study. Calves were randomly selected from 20 sub-locations and recruited within a week of birth from different farms over a 45 km radius area centered on Busia in the Western part of Kenya. The data comprised of 481.1 calf years of observation. Clinical examinations, sample collection and analysis were carried out at 5 week intervals, from birth until one year old. Cox proportional hazard models with frailty terms were used for the statistical analysis of risk factors. A standardized post-mortem examination was conducted on all animals that died during the study and appropriate samples collected.

RESULTS

The all-cause mortality rate was estimated at 16.1 (13.0-19.2; 95% CI) per 100 calf years at risk. The Cox models identified high infection intensity with Theileria spp., the most lethal of which causes East Coast Fever disease, infection with Trypanosome spp., and helminth infections as measured by Strongyle spp. eggs per gram of faeces as the three important infections statistically associated with infectious disease mortality in these calves. Analysis of post-mortem data identified East Coast Fever as the main cause of death accounting for 40% of all deaths, haemonchosis 12% and heartwater disease 7%.

CONCLUSION

The findings demonstrate the impact of endemic parasitic diseases in indigenous animals expected to be well adapted against disease pressures. Additionally, agreement between results of Cox models using data from simple diagnostic procedures and results from post-mortem analysis underline the potential use such diagnostic data to reduce calf mortality. The control strategies for the identified infectious diseases have been discussed.

Design and descriptive epidemiology of the Infectious Diseases of East African Livestock (IDEAL) project, a longitudinal calf cohort study in western Kenya

Background

There is a widely recognised lack of baseline epidemiological data on the dynamics and impacts of infectious cattle diseases in east Africa. The Infectious Diseases of East African Livestock (IDEAL) project is an epidemiological study of cattle health in western Kenya with the aim of providing baseline epidemiological data, investigating the impact of different infections on key responses such as growth, mortality and morbidity, the additive and/or multiplicative effects of co-infections, and the influence of management and genetic factors.

A longitudinal cohort study of newborn calves was conducted in western Kenya between 2007-2009. Calves were randomly selected from all those reported in a 2 stage clustered sampling strategy. Calves were recruited between 3 and 7 days old. A team of veterinarians and animal health assistants carried out 5-weekly, clinical and postmortem visits. Blood and tissue samples were collected in association with all visits and screened using a range of laboratory based diagnostic methods for over 100 different pathogens or infectious exposures.

Results

The study followed the 548 calves over the first 51 weeks of life or until death and when they were reported clinically ill. The cohort experienced a high all cause mortality rate of 16% with at least 13% of these due to infectious diseases. Only 307 (6%) of routine visits were classified as clinical episodes, with a further 216 reported by farmers. 54% of calves reached one year without a reported clinical episode. Mortality was mainly to east coast fever, haemonchosis, and heartwater. Over 50 pathogens were detected in this population with exposure to a further 6 viruses and bacteria.

Conclusion

The IDEAL study has demonstrated that it is possible to mount population based longitudinal animal studies. The results quantify for the first time in an animal population the high diversity of pathogens a population may have to deal with and the levels of co-infections with key pathogens such as Theileria parva. This study highlights the need to develop new systems based approaches to study pathogens in their natural settings to understand the impacts of co-infections on clinical outcomes and to develop new evidence based interventions that are relevant.

Identification of hard ticks (Acari: Ixodidae) and seroprevalence to Theileria parva in cattle raised in North Kivu Province, Democratic Republic of Congo

This study aimed to identify tick species and to determine their relationship with the Theileria parva seroprevalence in cattle raised under an extensive farming system in North Kivu Province, Democratic Republic of Congo in two agro-ecological zones namely medium (1,000-1,850 m) and high (>1,850 m) altitude. Among the 3,215 ticks collected on 482 animals, from February to April 2009, Rhipicephalus appendiculatus (64.26 %), the main vector of T. parva, was the most abundant species followed by Rhipicephalus decoloratus (35.49 %) and Amblyomma variegatum (0.25 %). The mean burden of R. appendiculatus tick per infested animal appeared significantly higher at medium (6.5 ± 0.22 ticks) than at high (0.07 ± 0.3 ticks) altitude (P < 0.05). However, an indirect fluorescent antibody test carried out on 450 blood samples revealed a global T. parva seroprevalence of 43 % (95 % CI: 38-47) which was not significantly (P > 0.05) different between medium (48.4 %; 95 % CI: 38-49) and high (41.9 %; 95 % CI: 35-49) altitude. These relatively low seroprevalences suggest that there is a state of endemicity to T. parva infection in the study area. The presence of the tick vector on animals was associated with an increased risk of being seropositive to T. parva infection (odds ratio = 2.04; 95 % CI: 1.8-2.3; P < 0.001). The results suggest the need for a longitudinal study to investigate the seasonal dynamics of tick species and T. parva infection. The rate of tick infection should also be evaluated in order to determine the intensity of T. parva transmission to cattle.

Environment and farm factors associated with exposure to Theileria parva infection in cattle under traditional mixed farming system in Mbeere District, Kenya

The objective of this study was to investigate the relationship between seroprevalence to Theileria parva infection in cattle and potential environmental and farm-level effects in 80 farms under traditional crop-livestock system in Mbeere District, Kenya. A standardized questionnaire was used to collect the effects characteristics as related to T. parva infection epidemiology. Serum samples were collected from 440 cattle of all ages for detection of T. parva antibodies by the enzyme-linked immunosorbent assay technique. The association between the variables was assessed using a generalized estimation equation logistic regression model. The overall T. parva seroprevalence, accounting for correlation of responses, was 19.3% (95% confidence interval (CI) 14%, 25%). Two variables, "administrative division" and "presence of the vector tick on the farm", were significantly associated with the T. parva seroresponse. Respectively, cattle from farms in Gachoka, Evurore, and Mwea divisions were (and their 95% CI) 1.3 (0.36, 4.8), 4.4 (1.2, 15.9), and 15.2 (4.9, 47.1) times more likely to be seropositive relative to those from Siakago Division (P = 0.000). Cattle from farms in which the vector tick was present were 2.9 (1.2, 6.7) times more likely to be seropositive (P = 0.011). Results of this study suggested that both environmental and farm factors may be associated with T. parva infection epidemiology in Mbeere District. Under such circumstances, characterization of environmental suitability for the vector tick and corresponding environment-specific farm management practices in the district is required both for improved understanding of the disease and in planning disease control programs.