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Article ; Online: Machine learning in molecular ecology.

Fountain-Jones, Nicholas M / Smith, Megan L / Austerlitz, Frédéric

2021 Volume 21, Issue 8, Page(s) 2589–2597

MeSH term(s)	Ecology ; Machine Learning
Language	English
Publishing date	2021-10-29
Publishing country	England
Document type	Editorial
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13532
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Article ; Online: SPECIES IN THE FECES: DNA METABARCODING TO DETECT POTENTIAL GASTROPOD HOSTS OF PARELAPHOSTRONGYLUS TENUIS Consumed By Moose (Alces Alces).

Garwood, Tyler J / Moore, Seth A / Fountain-Jones, Nicholas M / Larsen, Peter A / Wolf, Tiffany M

Journal of wildlife diseases

2023 Volume 59, Issue 4, Page(s) 640–650

Abstract: Our understanding of wildlife multihost pathogen transmission systems is often incomplete due to the difficulty of observing contact between hosts. Understanding these interactions can be critical for preventing disease-induced wildlife declines. The ... ...

Abstract	Our understanding of wildlife multihost pathogen transmission systems is often incomplete due to the difficulty of observing contact between hosts. Understanding these interactions can be critical for preventing disease-induced wildlife declines. The proliferation of high-throughput sequencing technologies provides new opportunities to better explore these cryptic interactions. Parelaphostrongylus tenuis, a multihost parasite, is a leading cause of death in some moose (Alces alces) populations threatened by local extinction in the midwestern and northeastern US and southeastern Canada. Moose contract P. tenuis by consuming infected gastropod intermediate hosts, but little is known about which gastropod species moose consume. To gain more insight, we used a genetic metabarcoding approach on 258 georeferenced and temporally stratified moose fecal samples collected May-October 2017-20 from a declining population in the north-central US. We detected moose consumption of three species of gastropods across five positive samples. Two of these (Punctum minutissimum and Helisoma sp.) have been minimally investigated for the ability to host P. tenuis, while one (Zonitoides arboreus) is a well-documented host. Moose consumption of gastropods documented herein occurred in June and September. Our findings prove that moose consume gastropod species known to become infected by P. tenuis and demonstrate that fecal metabarcoding can provide novel insight on interactions between hosts of a multispecies pathogen transmission system. After determining and improving test sensitivity, these methods may also be extended to document important interactions in other multihost disease systems.
MeSH term(s)	Animals ; DNA Barcoding, Taxonomic/veterinary ; Metastrongyloidea ; Animals, Wild ; DNA ; Deer/parasitology ; Feces/parasitology
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-08-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	410709-3
ISSN	1943-3700 ; 0090-3558
ISSN (online)	1943-3700
ISSN	0090-3558
DOI	10.7589/JWD-D-22-00120
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Article ; Online: Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions.

Fountain-Jones, Nicholas M / Giraud, Tatiana / Zinger, Lucie / Bik, Holly / Creer, Simon / Videvall, Elin

Molecular ecology

2023 Volume 33, Issue 2, Page(s) e17223

Abstract: The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include ...

Abstract	The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.
MeSH term(s)	Bacteria ; Microbiota/genetics ; Ecology
Language	English
Publishing date	2023-11-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.17223
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Article ; Online: Effect of molnupiravir on SARS-CoV-2 evolution in immunocompromised patients: a retrospective observational study.

Fountain-Jones, Nicholas M / Vanhaeften, Robert / Williamson, Jan / Maskell, Janelle / Chua, I-Ly J / Charleston, Michael / Cooley, Louise

The Lancet. Microbe

2024 Volume 5, Issue 5, Page(s) e452–e458

Abstract: Introduction: Continued SARS-CoV-2 infection among immunocompromised individuals is likely to play a role in generating genomic diversity and the emergence of novel variants. Antiviral treatments such as molnupiravir are used to mitigate severe COVID-19 ...

Abstract	Introduction: Continued SARS-CoV-2 infection among immunocompromised individuals is likely to play a role in generating genomic diversity and the emergence of novel variants. Antiviral treatments such as molnupiravir are used to mitigate severe COVID-19 outcomes, but the extended effects of these drugs on viral evolution in patients with chronic infections remain uncertain. This study investigates how molnupiravir affects SARS-CoV-2 evolution in immunocompromised patients with prolonged infections. Methods: The study included five immunocompromised patients treated with molnupiravir and four patients not treated with molnupiravir (two immunocompromised and two non-immunocompromised). We selected patients who had been infected by similar SARS-CoV-2 variants and with high-quality genomes across timepoints to allow comparison between groups. Throat and nasopharyngeal samples were collected in patients up to 44 days post treatment and were sequenced using tiled amplicon sequencing followed by variant calling. The UShER pipeline and University of California Santa Cruz genome viewer provided insights into the global context of variants. Treated and untreated patients were compared, and mutation profiles were visualised to understand the impact of molnupiravir on viral evolution. Findings: Patients treated with molnupiravir showed a large increase in low-to-mid-frequency variants in as little as 10 days after treatment, whereas no such change was observed in untreated patients. Some of these variants became fixed in the viral population, including non-synonymous mutations in the spike protein. The variants were distributed across the genome and included unique mutations not commonly found in global omicron genomes. Notably, G-to-A and C-to-T mutations dominated the mutational profile of treated patients, persisting up to 44 days post treatment. Interpretation: Molnupiravir treatment in immunocompromised patients led to the accumulation of a distinctive pattern of mutations beyond the recommended 5 days of treatment. Treated patients maintained persistent PCR positivity for the duration of monitoring, indicating clear potential for transmission and subsequent emergence of novel variants. Funding: Australian Research Council.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/drug effects ; SARS-CoV-2/immunology ; Retrospective Studies ; Antiviral Agents/therapeutic use ; Antiviral Agents/pharmacology ; Immunocompromised Host ; Hydroxylamines/therapeutic use ; Hydroxylamines/pharmacology ; COVID-19 Drug Treatment ; Male ; Cytidine/analogs & derivatives ; Cytidine/therapeutic use ; Cytidine/pharmacology ; Female ; Middle Aged ; Mutation ; Aged ; COVID-19/immunology ; COVID-19/virology ; Evolution, Molecular ; Adult ; Genome, Viral/genetics
Chemical Substances	Antiviral Agents ; molnupiravir (YA84KI1VEW) ; Hydroxylamines ; Cytidine (5CSZ8459RP)
Language	English
Publishing date	2024-03-22
Publishing country	England
Document type	Journal Article ; Observational Study ; Research Support, Non-U.S. Gov't
ISSN	2666-5247
ISSN (online)	2666-5247
DOI	10.1016/S2666-5247(23)00393-2
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Article ; Online: Interspecies bacterial communication produces a delicate balance between Vibrio cholerae and the chironomid egg mass microbiome.

Oliver, Jonathan D / Fountain-Jones, Nicholas M

Molecular ecology

2021 Volume 30, Issue 7, Page(s) 1571–1573

Abstract: The evolution of antimicrobial resistance in bacterial pathogens is considered by the World Health Organization to be one of the ten most concerning public health threats facing humanity (World Health Organization, 2020). Bacterial diseases previously ... ...

Abstract	The evolution of antimicrobial resistance in bacterial pathogens is considered by the World Health Organization to be one of the ten most concerning public health threats facing humanity (World Health Organization, 2020). Bacterial diseases previously controllable by antibiotics are resurging and treatment options are dwindling. Cholera is one such disease. Human pathogenic strains of Vibrio cholerae cause as many as 4 million cases of disease resulting in over 100,000 deaths each year (Ali et al. 2015) and multidrug-resistant V. cholerae is now established where pandemic cholera persists. Vibrio cholerae is fundamentally an aquatic species thriving in brackish and estuarial waters. Its environmental prevalence, together with both extracellular and intracellular infection of alternative arthropod and mollusc hosts, produces a highly complex ecological milieu that is not well understood. With the absence of reliable antibiotic-based treatment options, it is necessary to build a better understanding of V. cholerae biology and ecology in order to develop alternative methods for risk modelling and disease control. In this issue of Molecular Ecology, authors Sela, Hammer, and Halpern experimentally investigated a mechanism by which V. cholerae pathogenicity is affected by interspecies quorum sensing involving an array of bacterial species from the microbiome of an alternative arthropod host, the egg mass of a chironomid midge (Diptera:Chironomidae) (Sela et al. 2020). Quorum sensing is a mechanism whereby bacteria communicate with each other using autoinducers and is known to be important, for example, in shaping virulence in a variety of pathogenic bacteria. The innovative methodologies they used, both in molecular and protein biology and reductive investigative microbiomics, are helping to develop the tools needed for understanding this understudied ecological system and fighting cholera in a post-antibiotic world.
MeSH term(s)	Animals ; Chironomidae ; Communication ; Hemagglutinins ; Humans ; Microbiota ; Quorum Sensing ; Vibrio cholerae/genetics
Chemical Substances	Hemagglutinins
Language	English
Publishing date	2021-03-01
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.15839
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Article ; Online: Cross-sectional association of Toxoplasma gondii exposure with BMI and diet in US adults.

Cuffey, Joel / Lepczyk, Christopher A / Zhao, Shuoli / Fountain-Jones, Nicholas M

PLoS neglected tropical diseases

2021 Volume 15, Issue 10, Page(s) e0009825

Abstract: Toxoplasmosis gondii exposure has been linked to increased impulsivity and risky behaviors, which has implications for eating behavior. Impulsivity and risk tolerance is known to be related with worse diets and a higher chance of obesity. There is little ...

Abstract	Toxoplasmosis gondii exposure has been linked to increased impulsivity and risky behaviors, which has implications for eating behavior. Impulsivity and risk tolerance is known to be related with worse diets and a higher chance of obesity. There is little known, however, about the independent link between Toxoplasma gondii (T. gondii) exposure and diet-related outcomes. Using linear and quantile regression, we estimated the relationship between T. gondii exposure and BMI, total energy intake (kcal), and diet quality as measured by the Health Eating Index-2015 (HEI) among 9,853 adults from the 2009-2014 National Health and Nutrition Examination Survey. Previous studies have shown different behavioral responses to T. gondii infection among males and females, and socioeconomic factors are also likely to be important as both T. gondii and poor diet are more prevalent among U.S. populations in poverty. We therefore measured the associations between T. gondii and diet-related outcomes separately for men and women and for respondents in poverty. Among females <200% of the federal poverty level Toxoplasmosis gondii exposure was associated with a higher BMI by 2.0 units (95% CI [0.22, 3.83]) at median BMI and a lower HEI by 5.05 units (95% CI [-7.87, -2.24]) at the 25th percentile of HEI. Stronger associations were found at higher levels of BMI and worse diet quality among females. No associations were found among males. Through a detailed investigation of mechanisms, we were able to rule out T. gondii exposure from cat ownership, differing amounts of meat, and drinking water source as potential confounding factors; environmental exposure to T. gondii as well as changes in human behavior due to parasitic infection remain primary mechanisms.
MeSH term(s)	Adult ; Body Mass Index ; Cross-Sectional Studies ; Diet ; Female ; Humans ; Male ; Nutrition Surveys ; Obesity/economics ; Obesity/metabolism ; Obesity/parasitology ; Obesity/physiopathology ; Poverty ; Toxoplasma/genetics ; Toxoplasma/isolation & purification ; Toxoplasmosis/economics ; Toxoplasmosis/metabolism ; Toxoplasmosis/parasitology ; Toxoplasmosis/physiopathology ; Young Adult
Language	English
Publishing date	2021-10-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2727
ISSN (online)	1935-2735
ISSN	1935-2727
DOI	10.1371/journal.pntd.0009825
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Article: Comparative phylodynamics reveals the evolutionary history of SARS-CoV-2 emerging variants in the Arabian Peninsula.

Alkhamis, Moh A / Fountain-Jones, Nicholas M / Khajah, Mohammad M / Alghounaim, Mohammad / Al-Sabah, Salman K

Virus evolution

2022 Volume 8, Issue 1, Page(s) veac040

Abstract: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to be responsible for an unprecedented worldwide public health and economic catastrophe. Accurate understanding and comparison of global and regional evolutionary ... ...

Abstract	Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to be responsible for an unprecedented worldwide public health and economic catastrophe. Accurate understanding and comparison of global and regional evolutionary epidemiology of novel SARS-CoV-2 variants are critical to guide current and future interventions. Here, we utilized a Bayesian phylodynamic pipeline to trace and compare the evolutionary dynamics, spatiotemporal origins, and spread of five variants (Alpha, Beta, Delta, Kappa, and Eta) across the Arabian Peninsula. We found variant-specific signatures of evolution and spread that are likely linked to air travel and disease control interventions in the region. Alpha, Beta, and Delta variants went through sequential periods of growth and decline, whereas we inferred inconclusive population growth patterns for the Kappa and Eta variants due to their sporadic introductions in the region. Non-pharmaceutical interventions imposed between mid-2020 and early 2021 likely played a role in reducing the epidemic progression of the Beta and the Alpha variants. In comparison, the combination of the non-pharmaceutical interventions and the rapid rollout of vaccination might have shaped Delta variant dynamics. We found that the Alpha and Beta variants were frequently introduced into the Arab peninsula between mid-2020 and early 2021 from Europe and Africa, respectively, whereas the Delta variant was frequently introduced between early 2021 and mid-2021 from East Asia. For these three variants, we also revealed significant and intense dispersal routes between the Arab region and Africa, Europe, Asia, and Oceania. In contrast, the restricted spread and stable effective population size of the Kappa and the Eta variants suggest that they no longer need to be targeted in genomic surveillance activities in the region. In contrast, the evolutionary characteristics of the Alpha, Beta, and Delta variants confirm the dominance of these variants in the recent outbreaks. Our study highlights the urgent need to establish regional molecular surveillance programs to ensure effective decision making related to the allocation of intervention activities targeted toward the most relevant variants.
Language	English
Publishing date	2022-05-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veac040
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Garwood, Tyler J / Richards, Jessie E / Macchietto, Marissa G / Gerhold, Richard W / Kania, Stephen A / Garbe, John R / Fountain-Jones, Nicholas M / Larsen, Peter A / Wolf, Tiffany M

Journal of nematology

2024 Volume 56, Issue 1, Page(s) 20240009

Abstract: Parelaphostrongylus ... ...

Abstract	Parelaphostrongylus tenuis
Language	English
Publishing date	2024-03-14
Publishing country	Poland
Document type	Journal Article
ZDB-ID	410426-2
ISSN	0022-300X
ISSN	0022-300X
DOI	10.2478/jofnem-2024-0009
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Article ; Online: Anemia or other comorbidities? using machine learning to reveal deeper insights into the drivers of acute coronary syndromes in hospital admitted patients.

Alsayegh, Faisal / Alkhamis, Moh A / Ali, Fatima / Attur, Sreeja / Fountain-Jones, Nicholas M / Zubaid, Mohammad

PloS one

2022 Volume 17, Issue 1, Page(s) e0262997

Abstract: Acute coronary syndromes (ACS) are a leading cause of deaths worldwide, yet the diagnosis and treatment of this group of diseases represent a significant challenge for clinicians. The epidemiology of ACS is extremely complex and the relationship between ... ...

Abstract	Acute coronary syndromes (ACS) are a leading cause of deaths worldwide, yet the diagnosis and treatment of this group of diseases represent a significant challenge for clinicians. The epidemiology of ACS is extremely complex and the relationship between ACS and patient risk factors is typically non-linear and highly variable across patient lifespan. Here, we aim to uncover deeper insights into the factors that shape ACS outcomes in hospitals across four Arabian Gulf countries. Further, because anemia is one of the most observed comorbidities, we explored its role in the prognosis of most prevalent ACS in-hospital outcomes (mortality, heart failure, and bleeding) in the region. We used a robust multi-algorithm interpretable machine learning (ML) pipeline, and 20 relevant risk factors to fit predictive models to 4,044 patients presenting with ACS between 2012 and 2013. We found that in-hospital heart failure followed by anemia was the most important predictor of mortality. However, anemia was the first most important predictor for both in-hospital heart failure, and bleeding. For all in-hospital outcome, anemia had remarkably non-linear relationships with both ACS outcomes and patients' baseline characteristics. With minimal statistical assumptions, our ML models had reasonable predictive performance (AUCs > 0.75) and substantially outperformed commonly used statistical and risk stratification methods. Moreover, our pipeline was able to elucidate ACS risk of individual patients based on their unique risk factors. Fully interpretable ML approaches are rarely used in clinical settings, particularly in the Middle East, but have the potential to improve clinicians' prognostic efforts and guide policymakers in reducing the health and economic burdens of ACS worldwide.
MeSH term(s)	Acute Coronary Syndrome/mortality ; Acute Coronary Syndrome/therapy ; Aged ; Anemia/mortality ; Anemia/therapy ; Comorbidity ; Female ; Hospital Mortality ; Humans ; Machine Learning ; Male ; Middle Aged ; Middle East/epidemiology ; Models, Cardiovascular ; Patient Admission ; Registries ; Risk Assessment
Language	English
Publishing date	2022-01-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0262997
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Article ; Online: Positive associations matter: Microbial relationships drive tick microbiome composition.

Fountain-Jones, Nicholas M / Khoo, Benedict S / Rau, Austin / Berman, Jesse D / Burton, Erin N / Oliver, Jonathan D

Molecular ecology

2023 Volume 32, Issue 14, Page(s) 4078–4092

Abstract: Untangling how factors such as environment, host, associations among bacterial species and dispersal predict microbial composition is a fundamental challenge. In this study, we use complementary machine-learning approaches to quantify the relative role ... ...

Abstract	Untangling how factors such as environment, host, associations among bacterial species and dispersal predict microbial composition is a fundamental challenge. In this study, we use complementary machine-learning approaches to quantify the relative role of these factors in shaping microbiome variation of the blacklegged tick Ixodes scapularis. I. scapularis is the most important vector for Borrelia burgdorferi (the causative agent for Lyme disease) in the U.S. as well as a range of other important zoonotic pathogens. Yet the relative role of the interactions between pathogens and symbionts compared to other ecological forces is unknown. We found that positive associations between microbes where the occurrence of one microbe increases the probability of observing another, including between both pathogens and symbionts, was by far the most important factor shaping the tick microbiome. Microclimate and host factors played an important role for a subset of the tick microbiome including Borrelia (Borreliella) and Ralstonia, but for the majority of microbes, environmental and host variables were poor predictors at a regional scale. This study provides new hypotheses on how pathogens and symbionts might interact within tick species, as well as valuable predictions for how some taxa may respond to changing climate.
MeSH term(s)	Animals ; Lyme Disease/microbiology ; Ixodes/microbiology ; Borrelia burgdorferi/genetics ; Borrelia ; Microbiota/genetics
Language	English
Publishing date	2023-05-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.16985
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