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Background Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and antibiotic use, the role of household environments is still unclear. Furthermore, the development of the gut antimicrobial resistome and its role in health and disease is not well characterized, particularly in settings with water insecurity and less sanitation infrastructure. Results This study investigated the gut microbiome and resistome of infants and young children (ages 4 days-6 years) in rural Nicaragua using Oxford Nanopore Technology’s MinION long-read sequencing. Differences in gut microbiome diversity and antibiotic resistance gene (ARG) abundance were examined for associations with host factors (age, sex, height for age z-score, weight for height z-score, delivery mode, breastfeeding habits) and household environmental factors (animals inside the home, coliforms in drinking water, enteric pathogens in household floors, fecal microbial source tracking markers in household floors). We identified anticipated associations of higher gut microbiome diversity with participant age and vaginal delivery. However, novel to this study were the significant, positive associations between ruminant and dog fecal contamination of household floors and gut microbiome diversity. We also identified greater abundance of potential pathogens in the gut microbiomes of participants with higher fecal contamination on their household floors. Path analysis revealed that water quality and household floor contamination independently and significantly influenced gut microbiome diversity when controlling for age. These gut microbiome contained diverse resistome, dominated by multidrug, tetracycline, macrolide/lincosamide/streptogramin, and beta-lactam resistance. We found that the abundance of ARGs in the gut decreased with age. The bacterial hosts of ARGs were mainly from the family Enterobacteriaceae , particularly Escherichia coli . Conclusions This study identified the role of household environmental contamination in the developing gut microbiome and resistome of young children and infants with a One Health perspective. We found significant relationships between host age, gut microbiome diversity, and the resistome. Understanding the impact of the household environment on the development of the resistome and microbiome in early life is essential to optimize the relationship between environmental exposure and human health. 92Jf2w8Y_xc1zDLBRpWCqW Video Abstract Graphical Abstract

Background Reduced pelvic limb reflexes in dogs with spinal cord injury typically suggests a lesion of the L4‐S3 spinal cord segments. However, pelvic limb reflexes might also be reduced in dogs with a T3‐L3 myelopathy and concurrent spinal shock. Hypothesis/Objectives We hypothesized that statistical models could be used to identify clinical variables associated with spinal shock in dogs with spinal cord injuries. Animals Cohort of 59 dogs with T3‐L3 myelopathies and spinal shock and 13 dogs with L4‐S3 myelopathies. Methods Data used for this study were prospectively entered by partner institutions into the International Canine Spinal Cord Injury observational registry between October 2016 and July 2019. Univariable logistic regression analyses were performed to assess the association between independent variables and the presence of spinal shock. Independent variables were selected for inclusion in a multivariable logistic regression model if they had a significant effect (P ≤ .1) on the odds of spinal shock in univariable logistic regression. Results The final multivariable model included the natural log of weight (kg), the natural log of duration of clinical signs (hours), severity (paresis vs paraplegia), and pelvic limb tone (normal vs decreased/absent). The odds of spinal shock decreased with increasing weight (odds ratio [OR] = 0.28, P = .09; confidence interval [CI] 0.07‐1.2), increasing duration (OR = 0.44, P = .02; CI 0.21‐0.9), decreased pelvic limb tone (OR = 0.04, P = .003; CI 0.01‐0.36), and increased in the presence of paraplegia (OR = 7.87, P = .04; CI 1.1‐56.62). Conclusions and Clinical Importance A formula, as developed by the present study and after external validation, could be useful for assisting clinicians in determining the likelihood of spinal shock in various clinical scenarios and aid in diagnostic planning.

Data on vector-borne pathogens infecting dogs from sub-Saharan Africa is limited. In this study, we assessed the prevalence of VBPs, their associated risk factors, and pathogen interactions in domestic dogs. Whole blood samples were obtained for 1202 apparently healthy dogs in Chad from September to October 2021, and nucleic acids were extracted and then subjected to a targeted next-generation sequencing (tNGS) assay for detection of 15 VBPs. Overall, 88.7% of the dogs were positive for at least one pathogen, and 62.9% were coinfected with two or more VBPs. The most frequent pathogen detected was Hepatozoon canis in 62.4% of the dogs, Mycoplasma haemocanis in 59.2%, Anaplasma platys in 29.2%, Candidatus Mycoplasma haematoparvum in 21.2%, Ehrlichia canis in 20.3%, Babesia vogeli in 2.0% and Candidatus Mycoplasma turicensis in 1.5%. While most of the dogs (62.9%) were co-infected with two or more VBPs, having an infection with three pathogens (30.8%) was more common. According to multivariable logistic regression analysis, being a senior dog and residing in Chari Baguirmi south were identified as potential risk factors for infection by most of the pathogens. Network analyses revealed complex interactions suggesting facilitative associations among VBPs. These results are useful in expanding the knowledge of VBPs in Africa and establishing a baseline for downstream studies into hemotropic mycoplasmas.

The dynamics of infectious diseases are greatly influenced by the movement of both susceptible and infected hosts. To accurately represent disease dynamics among a mobile host population, detailed movement models have been coupled with disease transmission models. However, a number of different host movement models have been proposed, each with their own set of assumptions and results that differ from the other models. Here, we compare two movement models coupled to the same disease transmission model using network analyses. This application of network analysis allows us to evaluate the fit and accuracy of the movement model in a multilevel modeling framework with more detail than established statistical modeling fitting methods. We used data that detailed mobile pastoralists' movements as input for 100 stochastic simulations of a Spatio-Temporal Movement (STM) model and 100 stochastic simulations of an Individual Movement Model (IMM). Both models represent dynamic movement and subsequent contacts. We generated networks in which nodes represent camps and edges represent the distance between camps. We simulated pathogen transmission over these networks and tested five network metrics-strength, betweenness centrality, three-step reach, density, and transitivity-to determine which could predict disease simulation outcomes and thereby be used to correlate model simulation results with disease transmission simulations. We found that strength, network density, and three-step reach of movement model results correlated with the final epidemic size of outbreak simulations. Betweenness centrality only weakly correlated for the IMM model. Transitivity only weakly correlated for the STM model and time-varying IMM model metrics. We conclude that movement models coupled with disease transmission models can affect disease transmission results and should be carefully considered and vetted when modeling pathogen spread in mobile host populations. Strength, network density, and three-step reach can be used to evaluate movement models before disease simulations to predict final outbreak sizes. These findings can contribute to the analysis of multilevel models across systems.

Modeling the movements of humans and animals is critical to understanding the transmission of infectious diseases in complex social and ecological systems. In this paper, we focus on the movements of pastoralists in the Far North Region of Cameroon, who follow an annual transhumance by moving between rainy and dry season pastures. Describing, summarizing, and modeling the transhumance movements in the region are important steps for understanding the role these movements may play in the transmission of infectious diseases affecting humans and animals. We collected data on this transhumance system for four years using a combination of surveys and GPS mapping. An analysis on the spatial and temporal characteristics of pastoral mobility suggests four transhumance modes, each with its own properties. Modes M1 and M2 represent the type of transhumance movements where pastoralists settle in a campsite for a relatively long period of time (≥20 days) and then move around the area without specific directions within a seasonal grazing area. Modes M3 and M4 on the other hand are the situations when pastoralists stay in a campsite for a relatively short period of time (<20 days) when moving between seasonal grazing areas. These four modes are used to develop a spatial-temporal mobility (STM) model that can be used to estimate the probability of a mobile pastoralist residing at a location at any time. We compare the STM model with two reference models and the experiments suggest that the STM model can effectively capture and predict the space-time dynamics of pastoral mobility in our study area.

In this article, we consider the implications of Murray Last's (1981) Knowing About Not Knowing for the study of ethnoveterinary knowledge of mobile pastoralists in the Far North Region of Cameroon. Specifically, we ask two interrelated questions: (1) what is the nature of this knowledge, and (2) what is the best way to study it? We conducted a study of pastoralists' knowledge of human and animal infectious diseases to evaluate the claim that mobile pastoralists in the Chad Basin do not have a concept for zoonotic diseases. We used a combination of free lists and semi-structured interviews to study pastoralists' knowledge. The results suggest that pastoralists do not have a concept for zoonotic diseases. Moreover, we found considerable variation in pastoralists' ethnoveterinary knowledge and examples of not knowing, which contrasts with previous studies that do not describe much variation in ethnoveterinary knowledge. In our discussion, we consider to what extent descriptions of ethnoveterinary knowledge are the product of researchers' conceptual framework and methodology.

Foot-and-mouth disease (FMD) is one of the most economically significant global livestock diseases. In the U.S., economic optimization models run in 2011 demonstrate the highest mean epidemic impact of a potential FMD outbreak in California would occur in livestock-dense regions, resulting in national agriculture losses of $2.3 to $69.0 billion. In the case that an FMD outbreak occurred in the U.S., mass depopulation, carcass disposal, and disinfection protocols for infected premises have been designed to prevent further viral spread. Because the FMD virus (FMDV) is spread mechanically via the environment, characteristics of viral environmental stability are important. Temperature and adsorption to soil particles are reported to be the most important factors affecting general virus survival; however, how much these factors alter FMDV survival has not been tested. Soil samples were examined from typical U.S. regions containing the highest cattle population densities: Tennessee, Georgia, Nebraska, California, Pennsylvania, Kentucky, and Iowa. Soils were spiked with known quantities of FMDV and FMDV stability was evaluated over seven distinct time points between 0 hours and 12 days at incubation temperatures of 25°C and 37°C to represent a range of typical ambient temperatures during the summer. FMDV stability was quantified via virus titration. Virus decayed faster at higher ambient temperatures for all soils, but decay at 25°C was faster in some soils. Consequently, areas with high ambient temperatures may have lower between-farm transmission rates, slower outbreak spread, and simpler farm decontamination. This study provides a helpful exploration into understanding soil survival of the virus. Additional investigations into FMDV survival across different soil types will aid in developing better disinfection protocols and further refining regional viral transmission rate estimates.

Foot-and-Mouth Disease virus (FMDV) is endemic in several regions and is a virus that can persist in the environment dependent on pH, relative humidity (RH), temperature, and matrix (i.e., soil, water, or air). Our previously published analysis of available viral persistence data showed that persistence is likely affected by interactions between RH, temperature, and matrix. Understanding these relationships will aid efforts to eliminate FMD, which has significant impacts on economies and food security. In Cameroon, West Africa, the livestock system consists of mobile (transhumant), transboundary trade and sedentary herds. Studying this system can provide information about the patterns of environmental detection of FMDV RNA that may influence approaches to virus elimination on premises during an outbreak. To improve our understanding of these patterns, we collected samples from individuals, vehicles, and along cattle pathways at three sedentary herds beginning on day one of owner-reported outbreaks, ending by day 30, and tested for the presence of FMD viral RNA using rRT-PCR. Our analysis suggests that detection decreases in soil surface samples with increased distance from herd and time from the first report of disease. Whereas time but not distance decreases detection in air samples. Interaction of RH and temperature suggests increased detection at high temperatures (>24°C) and RH (>75%), providing us with new information about the patterns of FMD viral RNA detection in and around cattle herds that could help to inform targeted virus elimination strategies, such as location and application of disinfectants.

Foot-and-mouth disease virus (FMDV) causes morbidity and mortality in a range of animals and threatens local economies by acting as a barrier to international trade. The outbreak in the United Kingdom in 2001 that cost billions to control highlighted the risk that the pathogen poses to agriculture. In response, several mathematical models have been developed to parameterize and predict both transmission dynamics and optimal disease control. However, a lack of understanding of the multi-strain etiology prevents characterization of multi-strain dynamics. Here, we use data from FMDV serology in an endemic setting to probe strain-specific transmission and immunodynamics. Five serotypes of FMDV affect cattle in the Far North Region of Cameroon. We fit both catalytic and reverse catalytic models to serological data to estimate the force of infection and the rate of waning immunity, and to detect periods of sustained transmission. For serotypes SAT2, SAT3, and type A, a model assuming life-long immunity fit better. For serotypes SAT1 and type O, the better-fit model suggests that immunity may wane over time. Our analysis further indicates that type O has the greatest force of infection and the longest duration of immunity. Estimates for the force of infection were time-varying and indicated that serotypes SAT1 and O displayed endemic dynamics, serotype A displayed epidemic dynamics, and SAT2 and SAT3 did not sustain local chains of transmission. Since these results were obtained from the same population at the same time, they highlight important differences in transmission specific to each serotype. They also show that immunity wanes at rates specific to each serotype, which influences patterns of local persistence. Overall, this work shows that viral serotypes can differ significantly in their epidemiological and immunological characteristics. Patterns and processes that drive transmission in endemic settings must consider complex viral dynamics for accurate representation and interpretation.