Mercy Yvonne Akinyi

1. Cardiac rate and rhythm reveal how animals adapt physiologically to day-to-day challenges. Yet collecting these data in wild animals presents major challenges for long-term data collection and for retrieving the data noninvasively. 2. Here, we present a key advance for collecting and transmitting continuous, fine-scaled physiological data in wild animals over several months. Working in the Amboseli baboon population in Kenya, we implanted Bluetooth-enabled (BLE) physiologgers in three wild adult female baboons and paired these devices with collars that enabled remote data downloads via long-range wide area network (LoRaWAN). 3. The system allowed: (1) continuous data collection over 11 months; (2) data downloads at distances >100 m; (3) data uploads to a cloud server from a remote site with unreliable cellular service; and (4) reliable performance in the absence of permanent network infrastructure (e.g., no LoRaWAN tower). The resulting data are the first long-term cardiac data in a wild primate. We also present data from one female who left her social group for unknown reasons (baboons are highly social and females rarely leave their groups). While alone, she exhibited higher heart rate variability, lower activity, and evidence of disrupted sleep. 4. In sum, physiologgers paired with BLE and LoRaWAN overcome the limitations of prior devices and represent powerful tools for investigating long-term physiological change in wild animals.

Background: Insertable cardiac monitors (ICMs) provide fine-grained, continuous data on cardiac activity. These data have great potential to reveal individual physiology, energetics, and stress responses, with implications for animal health, cognition, welfare, and conservation. However, these devices must be tested for safety, accuracy, and biological validity before being deployed in new species. Here we do so for the Reveal LINQ ^TM ICM (Medtronic, Minneapolis, MN USA) over an 8-month period in 10 adult female baboons ( Papio anubis and P. cynocephalus ) at the Kenya Institute of Primate Research in Kenya. We also report data on heart rate, physical activity, and body temperature in unrestrained, conscious, captive baboons during their normal activities. Finally, we test how heart rate and activity levels are predicted by baboon species, body mass, time of day, ambient temperature, social dominance rank, and ovarian cycle phase. Results: The baboons had no adverse reactions to the Reveal LINQ ^TM ICM. Their mean daytime heart rates (HRs) ranged from 89.6 to 128.0 beats per minute (bpm), and their resting HRs ranged from 74.4 to 98.2 bpm. The fastest observed R-wave interval validated by electrocardiogram (ECG) was 230 milliseconds (ms) (260 bpm), and the slowest was 1270 ms (47.4 bpm). In terms of predictors of HR and activity, HR was highly individualized, while activity level was not: baboon identity explained 41% of the variation in HR, but identity only 2% of variation in activity levels. HR was positively correlated with physical activity and HR was highest during daylight hours when the baboons were more active. Dominant baboons had higher HRs controlling for activity and were more active than low ranking individuals. In terms of ovarian cycle phase, HR was higher when individuals were in the periovulatory and luteal phases of the ovarian cycle compared to the follicular phase. Conclusions: Our findings support the future use of ICMs to investigate physiological responses in baboons. These devices’ safety and validity represent the plausibility of understanding inter-individual and inter-species variation in heart rate and activity in response to variation in the external environment and in individual internal state.

Mastitis is a leading disease in dairy animals such as goats across the world. It is a unique disease because it can be caused by diverse types of bacteria. This study was carried out in Manyatta Sub-County in Embu County, a region where goat farming thrives. Farmers in Manyatta Sub-County have often been plagued by mastitis resulting in heavy financial losses and negatively impacting public health. The aim of this pilot study was to identify some of the common bacteria associated with mastitis in dairy goats within Manyatta Sub-County and testing their resistance profiles to generate preliminary data for combating mastitis in the region. A total of 17 goats were sampled for the study. Bacteria culturing and 16S rRNA sequencing were conducted to identify the causative bacteria. Select resistance genes were screened through PCR. Some of the bacteria identified from the study include: Staphylococcus aureus, Coagulase-negative Staphylococcus (CONS), Streptococcus uberis, Escherichia coli, Pseudomonas spp, Klebsiella, Aeromonas and Serattia spp. Serattia Spp. was the most abundant bacteria. Resistance genes detected include; blaSHV, aadA, tetA and tetE. 80% of the isolated pathogens were multi-drug resistant, highlighting the severity of mastitis in Manyatta.

Background: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While the composition of bacterial and viral components of animal microbiota are increasingly well understood, eukaryotic composition remains neglected. Here we characterized eukaryotic diversity in the microbiomes in wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, and season of sample collection. Results: We analyzed a total of 75 fecal samples collected between 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of samples, respectively. Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effect of season, host age, and host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples). Conclusions: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is essential for primate health monitoring and management strategies.

Background The focus on P. falciparum diagnosis has led to an underestimation of the global burden of malaria resulting from neglected Plasmodium species. However, there is still scarce data on the prevalence of P. ovale species (spp) globally. To address this knowledge gap, data collected from cross-sectional studies in Kilifi county were used to: 1) determine the prevalence of P. ovale spp infections; and 2) determine the sensitivity of different diagnostic assays in detecting P. ovale spp infections. Methods A total of 531 individuals were sampled across three study sites in Kilifi County, Kenya between 2009 and 2020. Blood smears were prepared from peripheral blood and screened for Plasmodium parasite stages using light microscopy. Molecular screening involved DNA extraction of dried blood spots and blood in ethylenediaminetetraacetic acid, polymerase chain reaction (PCR) using primers targeting the 18 small ribosomal subunit and sequencing. Results Microscopy screening revealed that the most prevalent species was P. falciparum (32.0%) followed by P. malariae (9.0%) and then P. ovale spp( 1.5%). PCR screening identified additional P. ovale spp positives cases. Overall PCR results indicate that43 (8.1%) out of the 531 individuals harbored P. ovale spp infection with the highest prevalence reported in the tertiary health facility, (14.6%, 95% CI 8-23.6%), followed by the primary health facility (8.3%, 95% CI 5.4-11.9%), and the community from a cross-sectional blood survey, (3.6%, 95% CI 1.2-8.2%). Microscopy screening for P. ovale spp had a low sensitivity of 7% (95% CI 1-19-30%) and a high specificity of 99% (95% CI 98-100%). Sequencing results confirmed the presence of P.ovale curtisi. Conclusions This study provides baseline data for P.ovale spp surveillance in Kilifi County, primarily using PCR to improve diagnosis. These results suggest that malaria elimination and eradication efforts should not only concentrate on P. falciparum but should embrace a holistic approach towards elimination of all Plasmodium spp.

The early-life environment can profoundly shape the trajectory of an animal’s life, even years or decades later. One mechanism proposed to contribute to these early-life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early-life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early-life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early-life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early-life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early-life effects on fitness-related traits.

Background The focus on P. falciparum diagnosis has led to an underestimation of the global burden of malaria resulting from neglected Plasmodium species. However, there is still scarce data on the prevalence of P. ovale globally. To address this knowledge gap, data collected from cross-sectional studies in Kilifi county were used to: 1) determine the prevalence of P. ovale species infections; and 2) determine the sensitivity of different diagnostic assays in detecting P. ovale species infections. Methods A total of 531 individuals were sampled across three study sites in Kilifi County, Kenya between 2009 and 2020. Blood smears were prepared from peripheral blood and screened for Plasmodium parasite stages using light microscopy. Molecular screening involved DNA extraction of dried blood spots and blood in ethylenediaminetetraacetic acid, polymerase chain reaction (PCR) using primers targeting the 18 small ribosomal subunit and sequencing. Results Microscopy screening revealed that the most prevalent species was P. falciparum (32.0%) followed by P. malariae (9.0%) and then P. ovale (1.5%). PCR screening identified additional P. ovale species positives cases. Overall PCR results indicate that43 (8.1%) out of the 531 individuals harbored P. ovale curtisi infection with the highest prevalence reported in the tertiary health facility, (14.6%, 95% CI 8-23.6%), followed by the primary health facility (8.3%, 95% CI 5.4-11.9%), and the community from a cross-sectional blood survey, (3.6%, 95% CI 1.2-8.2%). Microscopy screening for P. ovale had a low sensitivity of 7% (95% CI 1-19-30%) and a high specificity of 99% (95% CI 98-100%). Sequencing results confirmed the presence of P.ovale curtisi. Conclusions This study provides baseline data for P.ovale species surveillance in Kilifi County, primarily using PCR to improve diagnosis. These results suggest that malaria elimination and eradication efforts should not only concentrate on P. falciparum but should embrace a holistic approach towards elimination of all Plasmodium species.

Background: The focus on P. falciparum diagnosis has led to an underestimation of the global burden of malaria resulting from neglected Plasmodium species. However, there is still scarce data on the prevalence of P. ovale globally. To address this knowledge gap, data collected from cross-sectional studies in Kilifi county were used to: 1) determine the prevalence of P. ovale species infections; and 2) determine the sensitivity of different diagnostic assays in detecting P. ovale species infections. Methods: A total of 531 individuals were sampled across three study sites in Kilifi County, Kenya between 2009 and 2020. Blood smears were prepared from peripheral blood and screened for Plasmodium parasite stages using light microscopy. Molecular screening involved DNA extraction of dried blood spots and blood in ethylenediaminetetraacetic acid, polymerase chain reaction (PCR) using primers targeting the 18 small ribosomal subunit and sequencing. Results: Microscopy screening revealed that the most prevalent species was P. falciparum (32.0%) followed by P. malariae (9.0%) and then P. ovale (1.5%). PCR screening identified additional P. ovale species positives cases. Overall, 48 (8.2%) out of the 531 individuals harbored P. ovale species infection with the highest prevalence reported in the tertiary health facility, (14.6%, 95% CI 8-23.6%), followed by the primary health facility (8.6%, 95% CI 5.4-11.9%), and the community from a cross-sectional blood survey, (6.5%, 95% CI 3.0-11.8%). Microscopy screening for P. ovale had a low sensitivity of 7% (95% CI 1-19-30%) and a high specificity of 99% (95% CI 98-100%). Sequencing results confirmed the presence of P.ovale curtisi. Conclusions: This study provides baseline data for P. ovale species surveillance in Kilifi County, primarily using PCR to improve diagnosis. These results suggest that malaria elimination and eradication efforts should not only concentrate on P. falciparum but should embrace a holistic approach towards elimination of all Plasmodium species.

The early life environment can profoundly shape the trajectory of an animal’s life, even years or decades later. One mechanism proposed to contribute to these early life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early life effects on fitness-related traits. Significance statement: The environment animals face when young can affect how they function throughout life. Long-lasting changes in DNA methylation—a chemical mark deposited on DNA that can affect gene activity—have been hypothesized to contribute to early life effects. But evidence for persistent, early environment-associated differences in DNA methylation is lacking in wild animals. Here, we show that early life adversity in wild baboons predicts DNA methylation levels in adulthood, especially for animals born in low resource environments and drought conditions. We also show that some of the changes we observe in DNA methylation have the capacity to influence gene activity levels. Together, our results support the idea that early experiences can become biologically embedded in the genomes of wild animals.

This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.