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Article ; Online: Hidden Markov Model

Gary Xie / Jeanne M. Fair

BMC Research Notes, Vol 14, Iss 1, Pp 1-

a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes

2021 Volume 5

Abstract: Abstract Objective Currently, next generation sequencing (NGS) is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient identification of novel or diverged ... ...

Abstract	Abstract Objective Currently, next generation sequencing (NGS) is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient identification of novel or diverged pathogenomic compositions remains a big challenge. It is especially true for short DNA sequence fragments from NGS, since sequence similarity searching is vulnerable to false negatives or false positives, as is mismatching or matching with unrelated proteins. Therefore, this study aimed to establish a bioinformatics approach that can generate unique motif sequences for profiling searching, resulting in high specificity and sensitivity. Results In this study, we introduced a Shortest Unique Representative Hidden Markov Model (HMM) approach to identify bacterial toxin, virulence factor (VF), and antimicrobial resistance (AR) in short sequence reads. We first construct unique representative domain sequences of toxin genes, VFs, and ARs to avoid potential false positives, and then to use HMM models to accurately identify potential toxin, VF, and AR fragments. The benchmark shows this approach can achieve relatively high specificity and sensitivity if the appropriate cutoff value is applied. Our approach can be used to recognize the protein sequences of known toxins and pathogens, identifies their common characteristics and then searches for similar sequences in other organisms.
Keywords	Markov chains ; Biological toxins ; Virulence factors ; Pathogenicity ; Bacterial proteins ; Genetic markers ; Medicine ; R ; Biology (General) ; QH301-705.5 ; Science (General) ; Q1-390
Subject code	006
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Editorial

Jeanne M. Fair

Frontiers in Public Health, Vol

Biological Engagement Programs: Reducing Threats and Strengthening Global Health Security Through Scientific Collaboration

2017 Volume 5

Keywords	cooperative engagement ; emerging diseases ; biothreat ; Global Health Security Agenda ; One Health ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2017-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A scoping review of zoonotic parasites and pathogens associated with abattoirs in Eastern Africa and recommendations for abattoirs as disease surveillance sites

Katie A. Rodarte / Jeanne M. Fair / Bernard K. Bett / Susan D. Kerfua / Folorunso O. Fasina / Andrew W. Bartlow

Frontiers in Public Health, Vol

2023 Volume 11

Abstract: Abattoirs are facilities where livestock are slaughtered and are an important aspect in the food production chain. There are several types of abattoirs, which differ in infrastructure and facilities, sanitation and PPE practices, and adherence to ... ...

Abstract	Abattoirs are facilities where livestock are slaughtered and are an important aspect in the food production chain. There are several types of abattoirs, which differ in infrastructure and facilities, sanitation and PPE practices, and adherence to regulations. In each abattoir facility, worker exposure to animals and animal products increases their risk of infection from zoonotic pathogens. Backyard abattoirs and slaughter slabs have the highest risk of pathogen transmission because of substandard hygiene practices and minimal infrastructure. These abattoir conditions can often contribute to environmental contamination and may play a significant role in disease outbreaks within communities. To assess further the risk of disease, we conducted a scoping review of parasites and pathogens among livestock and human workers in abattoirs across 13 Eastern African countries, which are hotspots for zoonoses. Our search results (n = 104 articles) showed the presence of bacteria, viruses, fungi, and macroparasites (nematodes, cestodes, etc.) in cattle, goats, sheep, pigs, camels, and poultry. Most articles reported results from cattle, and the most frequent pathogen detected was Mycobacterium bovis, which causes bovine tuberculosis. Some articles included worker survey and questionnaires that suggested how the use of PPE along with proper worker training and safe animal handling practices could reduce disease risk. Based on these findings, we discuss ways to improve abattoir biosafety and increase biosurveillance for disease control and mitigation. Abattoirs are a ‘catch all’ for pathogens, and by surveying animals at abattoirs, health officials can determine which diseases are prevalent in different regions and which pathogens are most likely transmitted from wildlife to livestock. We suggest a regional approach to biosurveillance, which will improve testing and data gathering for enhanced disease risk mapping and forecasting. Next generation sequencing will be key in identifying a wide range of pathogens, rather than a ...
Keywords	abattoir ; slaughterhouses ; livestock ; zoonotic disease ; one health ; Public aspects of medicine ; RA1-1270
Subject code	630
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Long‐term variation in environmental conditions influences host–parasite fitness

Karen Musgrave / Andrew W. Bartlow / Jeanne M. Fair

Ecology and Evolution, Vol 9, Iss 13, Pp 7688-

2019 Volume 7703

Abstract: Abstract Long‐term data on host and parasite fitness are important for predicting how host–parasite interactions will be altered in an era of global change. Here, we use data collected from 1997 to 2013 to explore effects of changing environmental ... ...

Abstract	Abstract Long‐term data on host and parasite fitness are important for predicting how host–parasite interactions will be altered in an era of global change. Here, we use data collected from 1997 to 2013 to explore effects of changing environmental conditions on bird–blowfly interactions in northern New Mexico. The objectives of this study were to examine what climate variables influence blowfly prevalence and intensity and to determine whether blowflies and climate variables affect bird fledging success. We examined how temperature, precipitation, and drought affect two parasitic blowflies and their hosts, Western Bluebirds (Sialia mexicana) and Ash‐throated Flycatchers (Myiarchus cinerascens). We found that blowfly prevalence did not change over time. Blowfly intensity increased over time in bluebird nests, but not in flycatcher nests. More blowflies result in slightly higher fledging success in bluebirds, but not flycatchers. There was a significant interaction between blowflies and precipitation on bluebird fledging success. For flycatchers, there was a significant interaction between blowflies and temperature and between blowflies and drought severity on fledging success. Given that the southwest is projected to be hotter and have more frequent and prolonged droughts, we predict that flycatchers may be negatively impacted by blowflies if these trends continue. Future work should focus on investigating the role of both blowflies and climate on fledging success. Climate patterns may negatively impact host fitness through altered parasite pressure.
Keywords	blowflies ; climate ; environmental change ; host–parasite interactions ; nestlings ; parasites ; Ecology ; QH540-549.5
Subject code	333
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Individual Nest Site Preferences Do Not Explain Upslope Population Shifts of a Secondary Cavity-Nesting Species

Elisa J. Abeyta / Andrew W. Bartlow / Charles D. Hathcock / Jeanne M. Fair

Animals, Vol 11, Iss 2457, p

2021 Volume 2457

Abstract: Geographic ranges of plants and animals are shifting due to environmental change. While some species are shifting towards the poles and upslope in elevation, the processes leading to these patterns are not well known. We analyzed 22 years of western ... ...

Abstract	Geographic ranges of plants and animals are shifting due to environmental change. While some species are shifting towards the poles and upslope in elevation, the processes leading to these patterns are not well known. We analyzed 22 years of western bluebird ( Sialia mexicana ) data from a large nest box network in northern New Mexico at elevations between 1860 m and 2750 m. This population has shifted to higher elevations over time, but whether this is due to changes in nesting behavior and preference for higher elevation within the population or driven by immigration is unclear. We banded adults and nestlings from nest boxes and examined nesting location and elevation for individual birds captured two or more times. Most recaptured birds nested at the same nest boxes in subsequent years, and the number of birds that moved upslope did not significantly differ from the number that moved downslope. Fledglings moved greater distances and elevations than adults, but these movements were not upslope specific. Female fledglings showed greater changes in elevation and distance compared to male fledglings, but again, movements were not consistently upslope. The upslope shift in this population may be due to birds immigrating into the population and not from changes in individual nesting behavior.
Keywords	behavioral plasticity ; dispersal distance ; elevation change ; range shift ; climate change ; long-term monitoring ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
Subject code	590
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Global health security threats and related risks in Latin America

Kenneth B. Yeh / Falgunee K. Parekh / Brooke Borgert / Gene G. Olinger / Jeanne M. Fair

Global Security: Health, Science and Policy, Vol 6, Iss 1, Pp 18-

2021 Volume 25

Abstract: The costs of responding and mitigating the COVID-19 pandemic is a critical example of the need for continual investment for global health security (GHS) preparedness in today’s inter-connected world as exemplified earlier with Ebola, Zika, and H1N1. ... ...

Abstract	The costs of responding and mitigating the COVID-19 pandemic is a critical example of the need for continual investment for global health security (GHS) preparedness in today’s inter-connected world as exemplified earlier with Ebola, Zika, and H1N1. Microbial diversity including endemic and emerging infectious diseases unique to Latin America are well known. When combined with geopolitical, socioeconomic, and environmental factors, especially climate change and human migration, which are expanding the range of disease vectors and pathogens, the risk for infectious disease outbreaks greatly increases. Enhancing GHS requires a greater awareness and cooperation within the region as well as more effective infectious disease surveillance systems. Frameworks such as the International Health Regulations and Global Health Security Agenda underpin policies to strengthen health systems. Greater international cooperation aimed to effectively enhance infectious disease surveillance are pivotal to increasing trust among partner countries and strengthen health security systems and best practices to respond and mitigate infectious disease outbreaks. Here we discuss infectious disease threats and risks associated with the current socioeconomic and political climate that influence GHS in order to demonstrate the need for further investment.
Keywords	latin america ; global health security ; covid-19 ; infectious disease surveillance ; preparedness ; Public aspects of medicine ; RA1-1270 ; Military Science ; U
Subject code	300
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Taylor & Francis Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: How Cooperative Engagement Programs Strengthen Sequencing Capabilities for Biosurveillance and Outbreak Response

Andrew W. Bartlow / Earl A. Middlebrook / Alicia T. Romero / Jeanne M. Fair

Frontiers in Public Health, Vol

2021 Volume 9

Abstract: The threat of emerging and re-emerging infectious diseases continues to be a challenge to public and global health security. Cooperative biological engagement programs act to build partnerships and collaborations between scientists and health ... ...

Abstract	The threat of emerging and re-emerging infectious diseases continues to be a challenge to public and global health security. Cooperative biological engagement programs act to build partnerships and collaborations between scientists and health professionals to strengthen capabilities in biosurveillance. Biosurveillance is the systematic process of detecting, reporting, and responding to especially dangerous pathogens and pathogens of pandemic potential before they become outbreaks, epidemics, and pandemics. One important tool in biosurveillance is next generation sequencing. Expensive sequencing machines, reagents, and supplies make it difficult for countries to adopt this technology. Cooperative engagement programs help by providing funding for technical assistance to strengthen sequencing capabilities. Through workshops and training, countries are able to learn sequencing and bioinformatics, and implement these tools in their biosurveillance programs. Cooperative programs have an important role in building and sustaining collaborations among institutions and countries. One of the most important pieces in fostering these collaborations is trust. Trust provides the confidence that a successful collaboration will benefit all parties involved. With sequencing, this enables the sharing of pathogen samples and sequences. Obtaining global sequencing data helps to identify unknown etiological agents, track pathogen evolution and infer transmission networks throughout the duration of a pandemic. Having sequencing technology in place for biosurveillance generates the capacity to provide real-time data to understand and respond to pandemics. We highlight the need for these programs to continue to strengthen sequencing in biosurveillance. By working together to strengthen sequencing capabilities, trust can be formed, benefitting global health in the face of biological threats.
Keywords	cooperative threat reduction ; emerging diseases ; next generation sequencing ; pandemic preparedness ; One Health ; Public aspects of medicine ; RA1-1270
Subject code	306
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cooperative Research and Infectious Disease Surveillance

Falgunee K. Parekh / John Hay / Kairat Tabynov / Roger Hewson / Jeanne M. Fair / Sandra Essbauer / Kenneth B. Yeh

Frontiers in Public Health, Vol

A 2021 Epilogue

2022 Volume 9

Abstract: As the world looks forward to turning a corner in the face of the COVID-19 pandemic, it becomes increasingly evident that international research cooperation and dialogue is necessary to end this global catastrophe. Last year, we initiated a research ... ...

Abstract	As the world looks forward to turning a corner in the face of the COVID-19 pandemic, it becomes increasingly evident that international research cooperation and dialogue is necessary to end this global catastrophe. Last year, we initiated a research topic: “Infectious Disease Surveillance: Cooperative Research in Response to Recent Outbreaks, Including COVID-19,” which aimed at featuring manuscripts focused on the essential link between surveillance and cooperative research for emerging and endemic diseases, and highlighting scientific partnerships in countries under-represented in the scientific literature. Here we recognize the body of work published from our manuscript call that resulted in over 50 published papers. This current analysis describes articles and authors from a variety of funded and unfunded international sources. The work exemplifies successful research and publications which are frequently cooperative, and may serve as a basis to model further global scientific engagements.
Keywords	cooperative research ; global health security ; infectious disease surveillance ; scientific publication ; COVID-19 ; Public aspects of medicine ; RA1-1270
Subject code	001
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparing western (Megascops kennicottii) and whiskered (M. trichopsis) screech-owl microbiomes in southern Arizona using a novel 16S rRNA sequencing method

Andrew W. Bartlow / S. Kane Moser / Jeremy E. Ellis / Charles D. Hathcock / Jeanne M. Fair

Animal Microbiome, Vol 4, Iss 1, Pp 1-

2022 Volume 13

Abstract: Abstract Microbiomes are essential to a host’s physiology and health. Despite the overall importance of microbiomes to animal health, they remain understudied in wildlife. Microbiomes function as physical barriers to invading pathogens, and changes in ... ...

Abstract	Abstract Microbiomes are essential to a host’s physiology and health. Despite the overall importance of microbiomes to animal health, they remain understudied in wildlife. Microbiomes function as physical barriers to invading pathogens, and changes in the diversity or composition of microbes within a host may disrupt this barrier. In order to use microbiomes in wildlife ecology, knowledge of the natural variation within and among species is essential. We compare the diversity and composition of two avian species that share the same habitat and niche in our study area, the western screech-owl (Megascops kennicottii) and the whiskered screech-owl (M. trichopsis). We used a targeted 16S sequencing method to improve the taxonomic resolution of microbiomes. We found similar measures of alpha diversity between species and sample types (cloacal samples vs. fecal samples). However, there were significant differences in bacterial species richness among nestlings from different nest boxes, and the composition differed between the two bird species and among nestlings from different nest boxes. Western screech-owls had more variation in alpha diversity and composition and had fewer bacterial species in their core microbiome than whiskered screech-owls. Siblings are likely to yield similar findings for microbiomes; thus, sampling nestlings from different nests may be most informative for monitoring population-level changes.
Keywords	Gut microbiota ; Nestlings ; Next generation sequencing ; Microbial communities ; Wildlife ; Veterinary medicine ; SF600-1100 ; Microbiology ; QR1-502
Subject code	590
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The association between SAα2,3Gal occurrence frequency and avian influenza viral load in mallards (Anas platyrhynchos) and blue-winged teals (Spatula discors)

Amanda C. Dolinski / Mark D. Jankowski / Jeanne M. Fair / Jennifer C. Owen

BMC Veterinary Research, Vol 16, Iss 1, Pp 1-

2020 Volume 17

Abstract: Abstract Background Individual heterogeneity in pathogen load can affect disease transmission dynamics; therefore, identifying intrinsic factors responsible for variation in pathogen load is necessary for determining which individuals are prone to be ... ...

Abstract	Abstract Background Individual heterogeneity in pathogen load can affect disease transmission dynamics; therefore, identifying intrinsic factors responsible for variation in pathogen load is necessary for determining which individuals are prone to be most infectious. Because low pathogenic avian influenza viruses (LPAIV) preferentially bind to alpha-2,3 sialic acid receptors (SAα2,3Gal) in the intestines and bursa of Fabricius in wild ducks (Anas and Spatula spp.), we investigated juvenile mallards (Anas platyrhyncos) and blue-winged teals (Anas discors) orally inoculated with A/northern pintail/California/44221–761/2006 (H5N9) and the virus titer relationship to occurrence frequency of SAα2,3Gal in the intestines and bursa. To test the natural variation of free-ranging duck populations, birds were hatched and raised in captivity from eggs collected from nests of free-ranging birds in North Dakota, USA. Data generated from qPCR were used to quantify virus titers in cloacal swabs, ileum tissue, and bursa of Fabricius tissue, and lectin histochemistry was used to quantify the occurrence frequency of SAα2,3Gal. Linear mixed models were used to analyze infection status, species, and sex-based differences. Multiple linear regression was used to analyze the relationship between virus titer and SAα2,3Gal occurrence frequency. Results In mallards, we found high individual variation in virus titers significantly related to high variation of SAα2,3Gal in the ileum. In contrast to mallards, individual variation in teals was minimal and significant relationships between virus titers and SAα2,3Gal were not determined. Collectively, teals had both higher virus titers and a higher occurrence frequency of SAα2,3Gal compared to mallards, which may indicate a positive association between viral load and SAα2,3Gal. Statistically significant differences were observed between infected and control birds indicating that LPAIV infection may influence the occurrence frequency of SAα2,3Gal, or vice versa, but only in specific tissues. Conclusions The results of this study provide quantitative evidence that SAα2,3Gal abundance is related to LPAIV titers; thus, SAα2,3Gal should be considered a potential intrinsic factor influencing variation in LPAIV load.
Keywords	Avian ; Influenza ; Lectin histochemistry ; Super-shedder ; Veterinary medicine ; SF600-1100
Subject code	590
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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