Face mask sampling (FMS) for tuberculosis shows lower diagnostic sensitivity than sputum sampling in Guinea.

BACKGROUND: Pulmonary tuberculosis (PTB) diagnosis relies on sputum examination, a challenge in sputum-scarce patients. Alternative non-invasive sampling methods such as face mask sampling (FMS) have been proposed. OBJECTIVE: To evaluate the value of FMS for PTB diagnosis by assessing its agreement with sputum samples processed by GeneXpert MTB/RIF (Ultra)(Xpert) testing, and describe FMS sensitivity and specificity. METHODS: This was a prospective study conducted at the Carrière TB clinic in Guinea. Presumptive TB patients willing to participate were asked to wear a surgical mask containing a polyvinyl alcohol (PVA) strip for thirty minutes. Subsequently, two spot sputum samples were collected, of which one was processed by microscopy on site and the other by Xpert in Guinea's National Reference Laboratory of Mycobacteriology (LNRM). The first 30 FMS were processed at the Supranational Reference Laboratory in Antwerp, Belgium, and the following 118 FMS in the LNRM. RESULTS: One hundred fifty patients participated, of whom 148 had valid results for both mask and sputum. Sputum smear microscopy was positive for 47 (31.8%) patients while sputum-Xpert detected MTB in 54 (36.5%) patients. Among the 54 patients testing sputum-Xpert positive, 26 (48.1%) yielded a positive FMS-Xpert result, while four sputum-Xpert negative patients tested positive for FMS and 90 patients were Xpert-negative for both sputum and mask samples, suggesting a moderate level of agreement (k-value of 0.47). The overall mask sensitivity was 48.1%, with 95.7% specificity. CONCLUSION: In our setting, Xpert testing on FMS did not yield a high level of agreement to sputum sample.

Multi-locus genomic signatures of local adaptation to snow across the landscape in California populations of a willow leaf beetle.

Organisms living in mountains contend with extreme climatic conditions, including short growing seasons and long winters with extensive snow cover. Anthropogenic climate change is driving unprecedented, rapid warming of montane regions across the globe, resulting in reduced winter snowpack. Loss of snow as a thermal buffer may have serious consequences for animals overwintering in soil, yet little is known about how variability in snowpack acts as a selective agent in montane ecosystems. Here, we examine genomic variation in California populations of the leaf beetle Chrysomela aeneicollis, an emerging natural model system for understanding how organisms respond to climate change. We used a genotype-environment association approach to identify genomic signatures of local adaptation to microclimate in populations from three montane regions with variable snowpack and a coastal region with no snow. We found that both winter-associated environmental variation and geographical distance contribute to overall genomic variation across the landscape. We identified non-synonymous variation in novel candidate loci associated with cytoskeletal function, ion transport and membrane stability, cellular processes associated with cold tolerance in other insects. These findings provide intriguing evidence that variation in snowpack imposes selective gradients in montane ecosystems.

Transcriptomic evidence indicates that montane leaf beetles prioritize digestion and reproduction in a sex-specific manner during emergence from dormancy.

During winter, many organisms conserve resources by entering dormancy, suppressing metabolism and biosynthesis. The transition out of winter dormancy to summer activity requires a quick reversal of this suppression, in order to exploit now-favorable environmental conditions. To date, mechanisms by which winter climate variation affects this transition remains unelucidated. Here we experimentally manipulated snow cover for naturally overwintering montane leaf beetles (Chrysomela aeneicollis), and profiled changes in gene expression during the transition out of dormancy in spring. Upon emergence, beetles up-regulate transcripts associated with digestion and nutrient acquisition and down regulate those associated with lipid metabolism, suggesting a shift away from utilizing stored lipid and towards digestion of carbohydrate-rich host plant tissue. Development of digestive capacity is followed by up-regulation of transcripts associated with reproduction; a transition that occurs earlier in females than males. Snow manipulation strongly affected the ground thermal regime and correspondingly gene expression profiles, with beetles showing a delayed up-regulation of reproduction in the dry compared to snowy plots. This suggests that winter conditions can alter the timing and prioritization of processes during emergence from dormancy, potentially magnifying the effects of declining snow cover in the Sierra's and other snowy mountains.

Changes in mitochondrial function parallel life history transitions between flight and reproduction in wing polymorphic field crickets.

Mitochondria serve as critical producers of both cellular energy and metabolic precursors for biosynthesis required for organismal growth, activity, somatic maintenance, and reproduction. Consequently, variation in mitochondrial function is commonly associated with variation in life histories both within and across species. For instance, flight-capable, long-winged crickets have mitochondria with larger bioenergetic capacities than flightless, short-winged crickets investing in early lifetime fecundity instead of flight. However, we do not know whether differences in mitochondrial function associated with life history are fixed or result from flexible changes in metabolism throughout the life cycle. We measured mitochondrial function of fat body tissue across early adulthood of long-winged and short-winged crickets from two species of wing-polymorphic field crickets (Gryllus firmus and Gryllus lineaticeps). Fat body is a multifunctional organ that supports both flight and reproduction in insects. Consistent with flexibility in mitochondrial function specific for alternative life histories, the capacity for oxidative phosphorylation increases in mitochondria throughout early adulthood in the fat body of long-winged but not short-winged crickets. Furthermore, fat body mitochondrial oxidative phosphorylation capacities declined rapidly when long-wing crickets degraded their flight muscles and initiated large-scale oogenesis. This finding suggests that shifts in tissue function require a concurrent shift in mitochondrial function and that tissue-specific functional constraints may underpin the flight-oogenesis trade-off. In conclusion, changes in mitochondrial bioenergetics form a component of alternative life histories, indicating that mitochondrial function is dynamic and set to a level that matches current and future energy demands and biosynthetic requirements of life history.

Exhaled Mycobacterium tuberculosis Predicts Incident Infection in Household Contacts.

BACKGROUND: Halting transmission of Mycobacterium tuberculosis (Mtb) by identifying infectious individuals early is key to eradicating tuberculosis (TB). Here we evaluate face mask sampling as a tool for stratifying the infection risk of individuals with pulmonary TB (PTB) to their household contacts. METHODS: Forty-six sputum-positive PTB patients in The Gambia (August 2016-November 2017) consented to mask sampling prior to commencing treatment. Incident Mtb infection was defined in 181 of their 217 household contacts as QuantiFERON conversion or an increase in interferon-γ of ≥1 IU/mL, 6 months after index diagnosis. Multilevel mixed-effects logistical regression analysis with cluster adjustment by household was used to identify predictors of incident infection. RESULTS: Mtb was detected in 91% of PTB mask samples with high variation in IS6110 copies (5.3 × 102 to 1.2 × 107). A high mask Mtb level (≥20 000 IS6110 copies) was observed in 45% of cases and was independently associated with increased likelihood of incident Mtb infection in contacts (adjusted odds ratio, 3.20 [95% confidence interval, 1.26-8.12]; P = .01), compared with cases having low-positive/negative mask Mtb levels. Mask Mtb level was a better predictor of incident Mtb infection than sputum bacillary load, chest radiographic characteristics, or sleeping proximity. CONCLUSIONS: Mask sampling offers a sensitive and noninvasive tool to support the stratification of individuals who are most infectious in high-TB-burden settings. Our approach can provide better insight into community transmission in complex environments.

Exhaled SARS-CoV-2 RNA viral load kinetics measured by facemask sampling associates with household transmission.

OBJECTIVES: No studies have examined longitudinal patterns of naturally exhaled SARS-CoV-2 RNA viral load (VL) during acute infection. We report this using facemask sampling (FMS) and assessed the relationship between emitted RNA VL and household transmission. METHODS: Between December 2020 and February 2021, we recruited participants within 24 hours of a positive RT-qPCR on upper respiratory tract sampling (URTS) (day 0). Participants gave FMS (for 1 hour) and URTS (self-taken) on seven occasions up to day 21. Samples were analysed by RT-qPCR (from sampling matrix strips within the mask) and symptom diaries were recorded. Household transmission was assessed through reporting of positive URTS RT-qPCR in household contacts. RESULTS: Analysis of 203 FMS and 190 URTS from 34 participants showed that RNA VL peaked within the first 5 days following sampling. Concomitant URTS, FMS RNA VL, and symptom scores, however, were poorly correlated, but a higher severity of reported symptoms was associated with FMS positivity up to day 5. Of 28 participants who had household contacts, 12 (43%) reported transmission. Frequency of household transmission was associated with the highest (peak) FMS RNA VL obtained (negative genome copies/strip: 0% household transmission; 1 to 1000 copies/strip: 20%; 1001 to 10 000 copies/strip: 57%; >10 000 copies/strip: 75%; p = 0.048; age adjusted OR of household transmission per log increase in copies/strip: 4.97; 95% CI, 1.20-20.55; p = 0.02) but not observed with peak URTS RNA VL. DISCUSSION: Exhaled RNA VL measured by FMS is highest in early infection, can be positive in symptomatic patients with concomitantly negative URTS, and is strongly associated with household transmission.

Balancing Trade-Offs Imposed by Growth Media and Mass Spectrometry for Bacterial Exometabolomics.

The bacterial exometabolome consists of a vast array of specialized metabolites, many of which are only produced in response to specific environmental stimuli. For this reason, it is desirable to control the extracellular environment with a defined growth medium composed of pure ingredients. However, complex (undefined) media are expected to support the robust growth of a greater variety of microorganisms than defined media. Here, we investigate the trade-offs inherent to a range of complex and defined solid media for the growth of soil microorganisms, production of specialized metabolites, and detection of these compounds using direct infusion mass spectrometry. We find that complex media support growth of more soil microorganisms, as well as allowing for the detection of more previously discovered natural products as a fraction of total m/z features detected in each sample. However, the use of complex media often caused mass spectrometer injection failures and poor-quality mass spectra, which in some cases resulted in over a quarter of samples being removed from analysis. Defined media, while more limiting in growth, generated higher quality spectra and yielded more m/z features after background subtraction. These results inform future exometabolomic experiments requiring a medium that supports the robust growth of many soil microorganisms. IMPORTANCE Bacteria are capable of producing and secreting a rich diversity of specialized metabolites. Yet, much of their exometabolome remains hidden due to challenges associated with eliciting specialized metabolite production, labor-intensive sample preparation, and time-consuming analysis techniques. Using our versatile three-dimensional (3D)-printed culturing platform, SubTap, we demonstrate that rapid exometabolomic data collection from a diverse set of environmental bacteria is feasible. We optimized our platform by surveying Streptomyces isolated from soil on a variety of media types to assess viability, degree of specialized metabolite production, and compatibility with downstream LESA-DIMS analysis. Ultimately, this will enable data-rich experimentation, allowing for a better understanding of bacterial exometabolomes.

Life history strategy dictates thermal preferences across the diel cycle and in response to starvation in variable field crickets, Gryllus lineaticeps.

Insects behaviorally thermoregulate across the diel cycle, and their preferred microhabitats change based on current resources available and the thermal performance optima of traits. Specific combinations of traits being prioritized are set by life history strategies, making life history an important intrinsic determinant of thermal preferences. However, we do not know how life history strategies shape plasticity of behavioral thermoregulation, limiting our ability to predict responses to environmental variability. We compared female variable field crickets (Gryllus lineaticeps) that are flight-capable (long-winged) and flightless (short-winged) to test the hypothesis that life history strategy determines plasticity of thermal preferences across the diel cycle and following starvation. Thermal preferences were elevated during the nocturnal activity period, and long-winged crickets preferred warmer temperatures compared to short-winged crickets across the diel cycle when fully fed. However, thermal preferences of starved crickets were reduced compared to fed crickets. The reduction in thermal preferences was greater in long-winged crickets, resulting in similar thermal preferences between starved long- and short-winged individuals and reflecting a more plastic response. Thus, life history does determine plasticity in thermoregulatory behaviors following resource limitations and effects of life history on thermal preferences are context dependent.

Hypoxia Decreases Thermal Sensitivity and Increases Thermal Breadth of Locomotion in the Invasive Freshwater Snail Potamopyrgus antipodarum.

AbstractUnderstanding the physiology of invasive species will contribute to better prediction and prevention measures to avoid the economic and environmental consequences of biological invasions. Predicting the future range of Potamopyrgus antipodarum, a globally invasive aquatic snail, relies on a comprehensive understanding of its physiological tolerances to individual and combined environmental stressors. We conducted a laboratory study to investigate the interacting effects of temperature and dissolved oxygen in shaping the abiotic niche of P. antipodarum. We generated thermal performance curves (7°C-35°C) for resting respiration rate and voluntary locomotor behaviors under normoxia and hypoxia to find the conditions that limited each performance. Extreme high (>30°C) and low (<12°C) temperatures limited respiration and activity, but respiration rate was most oxygen sensitive at low temperatures. Under hypoxic conditions, activity was less thermally sensitive. Increased activity under high temperatures (22°C-28°C) may be fueled by anaerobic metabolism. Relying on anaerobic energy is a time-limited survival strategy, so further warming and deoxygenation of freshwater systems may limit the spread of this very tolerant invasive species.

Selection on dispersal drives evolution of metabolic capacities for energy production in female wing-polymorphic sand field crickets, Gryllus firmus.

Life history and metabolism covary, but the mechanisms and individual traits responsible for these linkages remain unresolved. Dispersal capability is a critical component of life history that is constrained by metabolic capacities for energy production. Conflicting relationships between metabolism and life histories may be explained by accounting for variation in dispersal and maximal metabolic rates. We used female wing-polymorphic sand field crickets, Gryllus firmus, selected either for long wings (LW, flight-capable) or short wings (SW, flightless) to test the hypothesis that selection on dispersal capability drives the evolution of metabolic capacities. While resting metabolic rates were similar, long-winged crickets reached higher maximal metabolic rates than short-winged crickets, resulting in improved running performance. We further provided insight into the mechanisms responsible for covariation between life history and metabolism by comparing mitochondrial content of tissues involved in powering locomotion and assessing the function of mitochondria isolated from long- and short-winged crickets. Our results demonstrated that larger metabolic capacities in long-winged crickets were underpinned by increases in mitochondrial content of dorsoventral flight muscle and enhanced bioenergetic capacities of mitochondria within the fat body, a tissue responsible for fuel storage and mobilization. Thus, selection on flight capability correlates with increases in maximal, but not resting metabolic rates, through modifications of tissues powering locomotion at the cellular and organelle levels. This allows organisms to meet high energetic demands of activity for life history. Dispersal capability should therefore explicitly be considered as a potential factor driving the evolution of metabolic capacities.

Aggregations reduce winter metabolic rates in the diapausing ladybeetle Hippodamia convergens.

Energy conservation is linked to survival and fitness of overwintering ectotherms, and is particularly critical in winter. Although many insects overwinter individually, some form aggregations with conspecifics. Aggregations cause metabolic suppression in some insects, but the effect of aggregations on metabolic rates and energy use in overwintering aggregations remains underexplored. The convergent ladybeetle (Hippodamia convergens) overwinters in massive aggregations, making it an ideal system for testing the effect of aggregation size on metabolic rates in overwintering insects. We measured metabolic rates of beetle aggregations of 1, 10, 25, and 50 individuals using stop-flow respirometry across two ecologically relevant temperatures, and measured locomotor activity as one possible driver of group effects on metabolic rate. Metabolic rates per beetle decreased with increasing aggregation size at both temperatures, but was more pronounced at low temperatures. Metabolic rates scaled hypometrically with mass, with deeper response at cool temperatures. Activity decreased with aggregation size, but only at low temperatures. These results suggest that individuals within aggregations enter a deeper metabolically inactive state that single individual beetles cannot achieve, which is partly but not completely explained by a reduction in locomotor activity. This group strategy for energy conservation may provide an additional selective advantage for the evolution of large overwintering aggregations.

The impact of metabolic plasticity on winter energy use models.

Understanding the energetic consequences of climate change is critical to identifying organismal vulnerabilities, particularly for dormant organisms relying on finite energy budgets. Ecophysiological energy use models predict long-term energy use from metabolic rate, but we do not know the degree to which plasticity in metabolism impacts estimates. We quantified metabolic rate-temperature relationships of dormant willow leaf beetles (Chrysomela aeneicollis) monthly from February to May under constant and variable acclimation treatments. Metabolic rate increased as diapause progressed, and acclimation to variable conditions altered both metabolic intensity and thermal sensitivity. However, incorporating these two types of metabolic plasticity into energy use models did not improve energy use estimates, validated by empirical measurements of energy stores. While metabolic rate-temperature relationships are plastic during winter, the magnitude of inter-individual variability in energy stores overshadows the effects of incorporating plasticity into energy use models, highlighting the importance of within-population variation in energy reserves.

Snow modulates winter energy use and cold exposure across an elevation gradient in a montane ectotherm.

Snow insulates the soil from air temperature, decreasing winter cold stress and altering energy use for organisms that overwinter in the soil. As climate change alters snowpack and air temperatures, it is critical to account for the role of snow in modulating vulnerability to winter climate change. Along elevational gradients in snowy mountains, snow cover increases but air temperature decreases, and it is unknown how these opposing gradients impact performance and fitness of organisms overwintering in the soil. We developed experimentally validated ecophysiological models of cold and energy stress over the past decade for the montane leaf beetle Chrysomela aeneicollis, along five replicated elevational transects in the Sierra Nevada mountains in California. Cold stress peaks at mid-elevations, while high elevations are buffered by persistent snow cover, even in dry years. While protective against cold, snow increases energy stress for overwintering beetles, particularly at low elevations, potentially leading to mortality or energetic tradeoffs. Declining snowpack will predominantly impact mid-elevation populations by increasing cold exposure, while high elevation habitats may provide refugia as drier winters become more common.

SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions.

Communication within the microbiome occurs through an immense diversity of small molecules. Capturing these microbial interactions is a significant challenge due to the complexity of the exometabolome and its sensitivity to environmental stimuli. Traditional methods for acquiring exometabolomic data from interacting microorganisms are limited by their low throughput or lack of sampling depth. To address this challenge, we introduce subtapping (short for substrate tapping), a technique for tapping into extracellular metabolites that are being transferred through the growth substrate during coculture. High-throughput subtapping is made possible by a new coculturing platform, named SubTap, that we engineered to resemble a 96-well plate. The three-dimensional (3D) printed SubTap platform captures the exometabolome in an agar compartment that connects physically separated growth chambers, which permits cell growth without competition for space. We show how SubTap facilitates replicable and quick detection of exometabolites via direct infusion mass spectrometry analysis. Using bacterial isolates from the soil, we apply SubTap to characterize the effects of growth medium, growth duration, and mixed versus unmixed coculturing on the exometabolome. Finally, we demonstrate SubTap's versatility by interrogating microbial interactions in multicultures with up to four strains. IMPORTANCE Improvements in experimental techniques and instrumentation have led to the discovery that the microbiome plays an essential role in human and environmental health. Nevertheless, there remain major impediments to conducting large-scale interrogations of the microbiome in a high-throughput manner, particularly in the field of exometabolomics. Existing methods to coculture microorganisms and interrogate their interactions are labor-intensive and low throughput. This inspired us to develop a solution for coculturing that was (i) open source, (ii) inexpensive, (iii) scalable, (iv) customizable, and (v) compatible with existing mass spectrometry instrumentation. Here, we present SubTap-a 3D printed coculturing platform that permits tapping directly into the growth substrate between physically separated, but interconnected, growth compartments. SubTap allows multiculture (with up to four distinct growth compartments) in spatially mixed or unmixed configurations and enables repeatable results with mass spectrometry, as shown by our validation with known compounds and cultures of one to four organisms.

Physiological demands and nutrient intake modulate a trade-off between dispersal and reproduction based on age and sex of field crickets.

Animals adjust resource acquisition throughout life to meet changing physiological demands of growth, reproduction, activity and somatic maintenance. Wing-polymorphic crickets invest in either dispersal or reproduction during early adulthood, providing a system in which to determine how variation in physiological demands, determined by sex and life history strategy, impact nutritional targets, plus the consequences of nutritionally imbalanced diets across life stages. We hypothesized that high demands of biosynthesis (especially oogenesis in females) drive elevated resource acquisition requirements and confer vulnerability to imbalanced diets. Nutrient targets and allocation into key tissues associated with life history investments were determined for juvenile and adult male and female field crickets (Gryllus lineaticeps) when given a choice between two calorically equivalent but nutritionally imbalanced (protein- or carbohydrate-biased) artificial diets, or when restricted to one imbalanced diet. Flight muscle synthesis drove elevated general caloric requirements for juveniles investing in dispersal, but flight muscle quality was robust to imbalanced diets. Testes synthesis was not costly, and life history investments by males were insensitive to diet composition. In contrast, costs of ovarian synthesis drove elevated caloric and protein requirements for adult females. When constrained to a carbohydrate-biased diet, ovary synthesis was reduced in reproductive morph females, eliminating their advantage in early life fecundity over the dispersal morph. Our findings demonstrate that nutrient acquisition modulates dispersal-reproduction trade-offs in an age- and sex-specific manner. Declines in food quality will thus disproportionately affect specific cohorts, potentially driving demographic shifts and altering patterns of life history evolution.