Biology subjects

Remais, J. V.

Publications and source records attributed to Remais, J. V..

9 recordsLinked to original sources

bioRxiv2026

Population structure of human-infecting and environmental isolates of Coccidioides immitis, the fungus causing Valley fever

Coccidioides is a soil-dwelling fungus that can cause serious disease (coccidioidomycosis or Valley fever) when its spores are inhaled. Limiting exposure to environmental spores is critical for disease prevention, yet how Coccidioides is distributed in the soil and where people become exposed remain almost entirely unknown. Here we report the first genomes of environmental isolates of C. immitis, from sampling of rodent burrows in the highly endemic region--California's San Joaquin Valley. We sequenced 16 soil-derived isolates alongside 26 novel patient-derived isolates collected from the same region to investigate genetic structure and diversity in C. immitis, and the potential origins of human infection. We found evidence of regional population structure among environmental C. immitis strains, though with extensive allele sharing between clusters. Most patient isolates derived nearly 100% of their ancestry from a genetic cluster shared with soil isolates, suggesting that the Coccidioides strain inhaled by a human host represents a random draw from the environmental pathogen pool. Further, we found that high levels of genomic diversity in environmental C. immitis are partitioned into effectively clonal lineages within individual rodent burrows, with isolates from neighboring burrows differing by over 13,000 SNPs. Together, these data support a picture of diverse, regionally structured environmental populations of C. immitis, suggesting that strategies to assign patient exposures to general regions within the San Joaquin Valley may be possible.

ecology↗

bioRxiv2026

Urban soils along the Kern River and Los Gatos Creek are hotspots for Coccidioides in the San Joaquin Valley of California

Coccidioidomycosis (Valley fever) is acquired through inhalation of spores produced by fungi in the genus Coccidioides. Coccidioides is commonly detected in, and cultivated from, the lung tissue of native rodents and the soils within their burrows. Coccidioidomycosis is acquired by exposure to environmentally produced spores and is not spread between hosts. Thus, determining the location of rodent burrows with soils harboring Coccidioides will be critical for understanding coccidioidomycosis incidence and modelling how Coccidioides distributions will be affected by global change. Coccidioides is readily detected in rodent burrows on undisturbed land, has not been detected on agricultural land, and is unstudied on urban land. To test the hypothesis that Coccidioides is in urban soil, we sampled rodent burrow soils from the banks of two water ways, the Kern River and Los Gatos Creek, which transect two cities, Bakersfield and Coalinga, in the San Joaquin Valley of California. To test the hypothesis that Coccidioides would not be detected at higher elevations, we extended our sampling of rodent burrows along waterways into the mountains of California. From 1178 soil and settled dust samples, we find that Coccidioides is found in urban riparian environments in Bakersfield and Coalinga, on riparian land on the floor of the San Joaquin Valley but not at higher elevations and is negatively correlated with modeled soil moisture. Coccidioides shows significant co-occurrence patterns with animal-associated fungal taxa, but no broader relationships with the greater fungal community. Our results warrant caution when excavating urban rodent burrows in the region. Author SummaryCoccidioidomycosis, or Valley fever, is caused by a fungus that primarily infects people when its spores become airborne and are inhaled. Although the fungus is found in the burrows of rodents, its presence in cities has been unclear. We investigated whether urban environments in Californias San Joaquin Valley, an area with high Valley fever incidence, harbor the fungus. By sampling more than a thousand soils and settled dust samples along riparian areas (waterways and adjacent environments) in Bakersfield and Coalinga, we found that the fungus that causes Valley fever, Coccidioides, occurs in urban riparian zones. The fungus was restricted to low elevations and was more likely to be detected in drier soils. We also compared positive and negative soils using DNA-based surveys of fungi. While the broader fungal community showed no strong relationship to Coccidioides, several species tied to animal activity were more common in positive samples, supporting a link to rodent hosts. These findings show that urban waterways can serve as habitat for Coccidioides. Because these areas lie within major population centers, identifying and avoiding disturbance of rodent burrows may reduce exposure risk, and future models of Valley fever should account for riparian corridors and local ecological conditions.

microbiology↗

bioRxiv2025

Climate warming and urbanization may expand dengue transmission risk in California

BackgroundWhile primarily a disease of tropical and subtropical regions, dengue outbreaks are increasing in non-endemic regions due to environmental change and increasing travel and trade. For these non-endemic regions, estimating the risk of dengue is challenging as transmission is driven by both local environmental conditions and the introduction of viremic travelers. In this study, we aimed to estimate current and future dengue risk in California, USA--a region that has recently experienced its first cases of locally-acquired dengue. MethodsWe modeled dengue risk as the product of three key components needed for local transmission--vector presence, temperature-suitability for pathogen transmission, and viral introductions via travel-associated cases--estimated using vector and case surveillance, sociodemographic, and environmental data. We estimated risk for locations and months where local transmission was reported in 2023-2024 to define a threshold level of risk. We then projected monthly, census tract-level risk under both current conditions and future scenarios of climate warming and urban expansion. FindingsApproximately 18.2 million (95% CI: 17.9-18.3) California residents--primarily in the Central Valley and the Los Angeles and San Diego metropolitan areas--currently live in areas where peak monthly dengue risk exceeds levels estimated during observed local transmission. Under moderate scenarios of climate warming and urban expansion, an additional 4.1 million (95% CI: 3.7-4.6) California residents may be at risk by mid-century, with the largest increase in risk estimated for September and for the Sacramento Valley and coastal southern California regions. Outside the summer months and beyond the Central Valley and southern California, current and future risk remains low due to one or more major bottlenecks to transmission. InterpretationOur study identifies the specific regions and months conducive to dengue transmission in the non-endemic setting of California. At present, this covers a substantial portion of the state and is projected to expand under on-going climate warming and urbanization. Our results underscore the need for sustained vector control, and timely detection and management of travel-associated cases. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSDengue is considered endemic in over 125 countries and rapidly expanding its range, aided by climate warming, urbanization, and global travel and trade. Estimating transmission risk in newly emerging regions is critical for public health preparedness and depends on both local environmental conditions and the introduction of viremic travelers. We searched PubMed from database inception to May 8, 2025, for articles published in English using search terms "dengue", "model", "non-endemic", and their common textual variants. We identified 75 relevant studies modeling dengue transmission risk in non-endemic settings. However, nearly all were focused on one or two major determinants of transmission (eg, climate, vector population dynamics, or case importations) and/or did not include future projections. We found no studies that developed and validated a model of dengue transmission risk in non-endemic settings that incorporated vector, pathogen, and human suitability factors, and applied this model to project future risk. Added value of this studyThis study provides a novel approach to model dengue transmission risk in emerging regions that integrates the major factors driving transmission--vector presence, temperature suitability, and travel-associated cases. We apply this model to California--an emerging center of transmission risk in the continental USA--to identify the times and regions where risk exceeds levels observed during recent local transmission. We found that approximately 18.2 million California residents may be at risk based on this threshold, with an additional 4.1 million potentially at risk by mid-century under a moderate scenario of warming and urban expansion. Implications of all the available evidenceOur study identifies the hotspots of dengue transmission risk at a fine spatial and temporal resolution (census tract, month) in a highly populous and globally-connected region of emerging dengue risk. These risk estimates, and the regionally-specific bottlenecks to transmission that we identify can inform targeted disease surveillance and prevention strategies. Further, our findings have implications for other emerging regions including the southern USA and southern Europe, suggesting that the risk of local dengue transmission may increase under ongoing climate warming, urbanization, and global travel.

ecology↗

bioRxiv2024

Detection of airborne Coccidioides spores using lightweight portable air samplers affixed to uncrewed aircraft systems in California's Central Valley

Coccidioidomycosis is an emerging fungal infection caused by inhalation of Coccidioides spp. spores. While airborne dispersal is critical to Coccidioides transmission, limited recovery of the pathogen from air has hindered understanding of the aerosolization and transport of spores. Here, we examine uncrewed aircraft systems (UAS) with portable, active air samplers as a novel means of capturing aerosolized Coccidioides and characterizing emissions and exposure risk. We sampled in September 2023 in eastern San Luis Obispo County, California, in an area with confirmed Coccidioides immitis in soils. We completed 41 20-minute flights across 14 sites using UAS equipped with an 8 L/min bioaerosol sampler and a low-cost particulate matter sensor. We sampled source soils and air under ambient conditions using one UAS at 1-10 m above ground level, and under a simulated high-dust event using two UAS, one at <2 m height and one at 5-12 m. We detected Coccidioides DNA in two of 41 air samples (4.9%), both under ambient conditions at 8 m above ground level, representing the highest known height of airborne Coccidioides detection. Spatially explicit UAS-based sampling could enhance understanding of Coccidioides aerobiology and enable detection in hard-to-reach or hazardous air masses, including dust storms and wildfire smoke. SynopsisUAS-based air sampling for bioaerosols, including pathogenic Coccidioides spp., opens new possibilities for characterizing the aerosolization and transport of fungal spores and other airborne pathogens.

ecology↗

bioRxiv2024

Characterizing the soil microbial community associated with the fungal pathogen Coccidioides immitis

Coccidioidomycosis is a fungal disease affecting humans and other mammals, caused by environmental pathogens of the genus Coccidioides. Understanding the ecological factors that shape the distribution of Coccidioides in soils is important for minimizing the risk of human exposure, though this remains challenging due to the pathogens highly variable spatial distribution. Here, we examined associations between the soil microbial community and Coccidioides immitis presence within the Carrizo Plain National Monument--a minimally disturbed grassland ecosystem, and the site of a longitudinal study examining the effects of rodents and their burrows on C. immitis presence in soils. Using internal transcribed spacer 2 (ITS2) and 16S sequencing to characterize the soil fungal and bacterial communities, we found over 30 fungal species, including several other members of the Onygenales order, that co-occurred with Coccidioides more frequently than expected by chance. Coccidioides-positive samples were significantly higher in microbial diversity than negative samples, an association partly driven by higher Coccidioides presence within rodent burrows compared to surface soils. Soil source (i.e., rodent burrow versus surface soil) explained the largest amount of variation in bacterial and fungal community diversity and composition, with soils collected from rodent burrows having higher microbial diversity than those collected from adjacent surface soils. While prior evidence is mixed regarding associations between Coccidioides and microbial diversity, our study suggests that favorable microhabitats such as rodent burrows can lead to a positive association between soil diversity and Coccidioides presence, particularly in otherwise resource-limited natural environments.

ecology↗

bioRxiv2024

Small mammals and their burrows shape the distribution of Coccidioides in soils: a long-term ecological experiment

BackgroundFor nearly all human fungal pathogens, the environmental constraints on their distributions remain poorly understood, hindering disease management. Here, we investigated the role of zoonotic host presence, soil conditions, and their interaction on the presence of Coccidioides immitis - an emerging fungal pathogen and causative agent of coccidioidomycosis. MethodsA long-term experimental study initiated in 2007 in the Carrizo Plain National Monument, California excluded rodents from certain areas (20 by 20-meter exclosures; n = 20) via the installation of submerged mesh fences, leaving emptied burrows intact. We collected 1,988 soil samples over four sampling periods spanning April 2021 to April 2022 using a factorial design that crossed burrows and surface soils (i.e., top 10 cm of soil) with exclosures (i.e., rodent absence) and non-exclosures (i.e., rodent presence). We measured in situ soil moisture, temperature, and vegetation, and analyzed soils for C. immitis DNA. ResultsThe proportion of samples containing C. immitis was significantly higher (p <0.0001) in burrow samples taken from outside rodent exclosures (i.e., rodents present; 28.5% positive) compared to burrow samples taken from within exclosures (i.e., rodents absent; 19.7%), surface soils outside of exclosures (3.6%) and surface soils within exclosures (0.5%). In generalized linear mixed models adjusting for soil conditions, rodent presence, and sample type (burrow vs. surface soil), we estimated that the odds of detecting C. immitis were 19.2 (95% CI: 11.3 - 36.7, p < 0.0001) times higher in soils taken from burrows compared to surface soils, and 2.6 (95% CI: 1.0 - 5.6, p = 0.049) times higher in soils where rodents were present compared to absent. Soil moisture was the only abiotic factor associated with C. immitis detection (odds ratio per 1% increase in water content: 0.83, 95% CI: 0.70 - 0.89, p = 0.0002). In mediation analyses, we estimated that 73.7% (95% CI: 68.9, 78.5) of the total association between rodents and Coccidioides detection effect was attributable to rodent creation of burrows. ConclusionsRodent creation and occupation of burrows substantially increases C. immitis detection. Synergy between reservoir host presence and environmental conditions may exist for other human fungal pathogens.

ecology↗

bioRxiv2021

Identifying low risk insecticides to address both food shortages and the biocontrol of human schistosomiasis

Use of agrochemicals, including insecticides, is vital to food production and predicted to increase 2-5 fold by 2050. Previous studies have shown a positive association between agriculture and the human infectious disease schistosomiasis, which is problematic as this parasitic disease infects approximately 250 million people worldwide. Certain insecticides might runoff fields and be highly toxic to invertebrates, such as prawns in the genus Macrobrachium, that are biocontrol agents for snails that transmit the parasites causing schistosomiasis. We used a laboratory dose-response experiment and an observational field study to determine the relative toxicities of three pyrethroid (esfenvalerate, {lambda}-cyhalothrin, and permethrin) and three organophosphate (chlorpyrifos, malathion, and terbufos) insecticides to Macrobrachium prawns. In the lab, pyrethroids were consistently several orders of magnitude more toxic than organophosphate insecticides, and more likely to runoff fields at lethal levels according to modeling data. In the field, we found that Macrobrachium prawn survival at 31 water contact sites in the lower basin of the Senegal River where schistosomiasis is endemic was predicted by pyrethroid application rates to nearby crop fields after controlling for abiotic and prawn-level factors. Our findings suggest that widely used pyrethroid insecticides can have strong non-target effects on Macrobrachium prawns that are biocontrol agents where 400 million people are at risk of human schistosomiasis. Understanding the ecotoxicology of high-risk insecticides may help improve human health in schistosomiasis-endemic regions undergoing agricultural expansion.

ecology↗

bioRxiv2018

Prawn aquaculture as a method for schistosomiasis control and poverty alleviation: a win-win approach to address a critical infectious disease of poverty

Recent evidence suggests crustacean snail predators may aid schistosomiasis control programs by targeting the environmental component of the parasites life cycle through predation of the snail species that serve as intermediate hosts of the parasite. We evaluate costs, benefits, and potential synergies between schistosomiasis control and aquaculture of giant prawns using an integrated bio-economic-epidemiologic model. We identified combinations of stocking density and aquaculture cycle length that maximize profit and offer disease control benefits for sustainable schistosomiasis control. We consider two prawn species in sub-Saharan Africa: the endemic, non-domesticated Macrobrachium vollenhovenii, and the non-native, domesticated Macrobrachium rosenbergii. We find that, at profit-optimal densities, both M. rosenbergii and M. vollenhovenii can complement conventional control approaches (mass drug treatment of people) and lead to sustainable schistosomiasis control. We conclude that integrated aquaculture strategies can be a win-win strategy in terms of health and sustainable development in schistosomiasis endemic regions of the world.

epidemiology↗

bioRxiv2017

Agrochemical pollution increases risk of human exposure to schistosome parasites

Roughly 10% of the global population is at risk of schistosomiasis, a snail-borne parasitic disease that ranks among the most important water-based diseases of humans in developing countries1-3. Increased prevalence, infection intensity, and spread of human schistosomiasis to non-endemic areas has been consistently linked with water resource management related to agricultural expansion, such as dam construction, which has resulted in increased snail habitat1,4-6. However, the role of agrochemical pollution in human schistosome transmission remains unexplored, despite strong evidence of agrochemicals increasing snail-borne diseases of wildlife7-9 and a projected 2- to 5-fold increase in global agrochemical use by 205010 that will disproportionately occur in schistosome-endemic regions. Using a field mesocosm experiment, we show that environmentally relevant concentrations of fertilizer, the common herbicide atrazine, and the common insecticide chlorpyrifos, individually and as mixtures, increase densities of schistosome-infected snails by increasing the algae snails eat (fertilizer and atrazine) and decreasing densities of snail predators (chlorpyrifos). Epidemiological models indicate that these agrochemical effects can increase transmission of schistosomiasis. Hence, the rapid agricultural changes occurring in schistosome-endemic regions11,12 that are driving increased agrochemical use and pollution could potentially increase the burden of schistosomiasis in these areas. Identifying agricultural practices or agrochemicals that minimize disease risk will be critical to meeting growing food demands while improving human wellbeing13,14.

ecology↗