Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and ß-lactam antibiotics.

The inoculum effect has been observed for nearly all antibiotics and bacterial species. However, explanations accounting for its occurrence and strength are lacking. We previously found that growth productivity, which captures the relationship between [ATP] and growth, can account for the strength of the inoculum effect for bactericidal antibiotics. However, the molecular pathway(s) underlying this relationship, and therefore determining the inoculum effect, remain undiscovered. We show that nucleotide synthesis can determine the relationship between [ATP] and growth, and thus the strength of inoculum effect in an antibiotic class-dependent manner. Specifically, and separate from activity through the tricarboxylic acid cycle, we find that transcriptional activity of genes involved in purine and pyrimidine synthesis can predict the strength of the inoculum effect for ß-lactam and aminoglycosides antibiotics, respectively. Our work highlights the antibiotic class-specific effect of purine and pyrimidine synthesis on the severity of the inoculum effect and paves the way for intervention strategies to reduce the inoculum effect in the clinic.

Partial trailside Japanese barberry (Ranunculales: Berberidaceae) removal did not reduce the abundance of questing blacklegged ticks (Acari: Ixodidae).

In a nature reserve in southern Maine, we removed invasive Japanese barberry (Berberis thunbergii de Candolle) along sections of forested recreational trails that ran through dense barberry infestations. Barberry thickets provide questing substrate and a protective microclimate for blacklegged ticks (Ixodes scapularis Say), and trail users could brush up against encroaching barberry and acquire ticks. Trailside barberry removal will reduce or eliminate encroaching tick questing substrate and could reduce trailside questing tick abundance by creating a microclimate more hostile to ticks. The same-day cut-and-spray treatment comprised mechanical cutting of barberry clumps (individual plants with numerous ramets) followed immediately by targeted herbicide application to the resulting root crowns. The treatment created trail shoulders to a lateral width of 1-2 m on both sides of 100-m trail sections, with initial treatment in the fall of 2013 and one retreatment in the summer of 2014. Our aim was to remove 90% of barberry clumps to achieve a 50% or better reduction in questing tick abundance on trail shoulders. However, by the fall of 2015, there were only 41% fewer barberry clumps on treated vs. untreated trail sections and there was no reduction in either adults or nymphs. We concluded that our barberry treatment protocol was not sufficiently aggressive since the resulting ecotone habitat on trail shoulders proved suitable for questing I. scapularis. In principle, cutting back barberry along trails should reduce trail user contact with questing deer ticks, but we were unable to demonstrate a reduction in trailside tick abundance.

Sub-inhibitory antibiotic treatment selects for enhanced metabolic efficiency.

Bacterial growth and metabolic rates are often closely related. However, under antibiotic selection, a paradox in this relationship arises: antibiotic efficacy decreases when bacteria are metabolically dormant, yet antibiotics select for resistant cells that grow fastest during treatment. That is, antibiotic selection counterintuitively favors bacteria with fast growth but slow metabolism. Despite this apparent contradiction, antibiotic resistant cells have historically been characterized primarily in the context of growth, whereas the extent of analogous changes in metabolism is comparatively unknown. Here, we observed that previously evolved antibiotic-resistant strains exhibited a unique relationship between growth and metabolism whereby nutrient utilization became more efficient, regardless of the growth rate. To better understand this unexpected phenomenon, we used a simplified model to simulate bacterial populations adapting to sub-inhibitory antibiotic selection through successive bottlenecking events. Simulations predicted that sub-inhibitory bactericidal antibiotic concentrations could select for enhanced metabolic efficiency, defined based on nutrient utilization: drug-adapted cells are able to achieve the same biomass while utilizing less substrate, even in the absence of treatment. Moreover, simulations predicted that restoring metabolic efficiency would re-sensitize resistant bacteria exhibiting metabolic-dependent resistance; we confirmed this result using adaptive laboratory evolutions of Escherichia coli under carbenicillin treatment. Overall, these results indicate that metabolic efficiency is under direct selective pressure during antibiotic treatment and that differences in evolutionary context may determine both the efficacy of different antibiotics and corresponding re-sensitization approaches.IMPORTANCEThe sustained emergence of antibiotic-resistant pathogens combined with the stalled drug discovery pipelines highlights the critical need to better understand the underlying evolution mechanisms of antibiotic resistance. To this end, bacterial growth and metabolic rates are often closely related, and resistant cells have historically been characterized exclusively in the context of growth. However, under antibiotic selection, antibiotics counterintuitively favor cells with fast growth, and slow metabolism. Through an integrated approach of mathematical modeling and experiments, this study thereby addresses the significant knowledge gap of whether antibiotic selection drives changes in metabolism that complement, and/or act independently, of antibiotic resistance phenotypes.

A molecular analysis of substituted phenylethylamines as potential microtubule targeting agents through in silico methods and in vitro microtubule-polymerization activity.

Natural phenethylamines are trace amine neurotransmitters associated with dopamine transmission and related illnesses such Parkinson's disease, and addiction. Synthetic phenethylamines can have psychoactive and hallucinogenic effects due to their high affinity with the 5-HT2A receptor. Evidence indicates phenethylamines can directly alter the microtubule cytoskeleton being structurally similar to the microtubule destabilizing agent colchicine, however little work has been done on this interaction. As microtubules provide neuron structure, intracellular transport, and influence synaptic plasticity the interaction of phenethylamines with microtubules is important for understanding the potential harms, or potential pharmaceutical use of phenethylamines. We investigated 110 phenethylamines and their interaction with microtubules. Here we performed molecular docking of these compounds at the colchicine binding site and ranked them via binding energy. The top 10% of phenethylamines were further screened based on pharmacokinetic and physicochemical properties derived from SwissADME and LightBBB. Based on these properties 25B-NBF, 25C-NBF, and DMBMPP were tested in in vitro microtubule polymerization assays showing that they alter microtubule polymerization dynamics in a dose dependent manner. As these compounds can rapidly cross the blood brain barrier and directly affect cytoskeletal dynamics, they have the potential to modulate cytoskeletal based neural plasticity. Further investigations into these mechanisms are warranted.

Universal equation of state for wave turbulence in a quantum gas.

Boyle's 1662 observation that the volume of a gas is, at constant temperature, inversely proportional to pressure, offered a prototypical example of how an equation of state (EoS) can succinctly capture key properties of a many-particle system. Such relationships are now cornerstones of equilibrium thermodynamics1. Extending thermodynamic concepts to far-from-equilibrium systems is of great interest in various contexts, including glasses2,3, active matter4-7 and turbulence8-11, but is in general an open problem. Here, using a homogeneous ultracold atomic Bose gas12, we experimentally construct an EoS for a turbulent cascade of matter waves13,14. Under continuous forcing at a large length scale and dissipation at a small one, the gas exhibits a non-thermal, but stationary, state, which is characterized by a power-law momentum distribution15 sustained by a scale-invariant momentum-space energy flux16. We establish the amplitude of the momentum distribution and the underlying energy flux as equilibrium-like state variables, related by an EoS that does not depend on the details of the energy injection or dissipation, or on the history of the system. Moreover, we show that the equations of state for a wide range of interaction strengths and gas densities can be empirically scaled onto each other. This results in a universal dimensionless EoS that sets benchmarks for the theory and should also be relevant for other turbulent systems.

Periodically disturbing biofilms reduces expression of quorum sensing-regulated virulence factors in Pseudomonas aeruginosa.

Pseudomonas aeruginosa uses quorum sensing to regulate the expression of virulence factors. In static environments, spatial structures, such as biofilms, can increase the expression of these virulence factors. However, in natural settings, biofilms are exposed to physical forces that disrupt spatial structure, which may affect the expression of virulence factors regulated by quorum sensing. We show that periodically disturbing biofilms composed of P. aeruginosa using a physical force reduces the expression of quorum sensing-regulated virulence factors. At an intermediate disturbance frequency, the expression of virulence factors in the las, rhl, and pqs regulons is reduced. Mathematical modeling suggests that perturbation of the pqsR receptor is critical for this reduction. Removing the lasR receptor enhances the reduction in the expression of virulence factors as a result of disturbance. Our results allow identification of environments where virulence is reduced and implicate the lasR receptor as having a buffering role against disturbance.

Interactions between metabolism and growth can determine the co-existence of Staphylococcus aureus and Pseudomonas aeruginosa.

Most bacteria exist and interact within polymicrobial communities. These interactions produce unique compounds, increase virulence and augment antibiotic resistance. One community associated with negative healthcare outcomes consists of Pseudomonas aeruginosa and Staphylococcus aureus. When co-cultured, virulence factors secreted by P. aeruginosa reduce metabolism and growth in S. aureus. When grown in vitro, this allows P. aeruginosa to drive S. aureus toward extinction. However, when found in vivo, both species can co-exist. Previous work has noted that this may be due to altered gene expression or mutations. However, little is known about how the growth environment could influence the co-existence of both species. Using a combination of mathematical modeling and experimentation, we show that changes to bacterial growth and metabolism caused by differences in the growth environment can determine the final population composition. We found that changing the carbon source in growth media affects the ratio of ATP to growth rate for both species, a metric we call absolute growth. We found that as a growth environment increases the absolute growth for one species, that species will increasingly dominate the co-culture. This is due to interactions between growth, metabolism, and metabolism-altering virulence factors produced by P. aeruginosa. Finally, we show that the relationship between absolute growth and the final population composition can be perturbed by altering the spatial structure in the community. Our results demonstrate that differences in growth environment can account for conflicting observations regarding the co-existence of these bacterial species in the literature, provides support for the intermediate disturbance hypothesis, and may offer a novel mechanism to manipulate polymicrobial populations.

Infections caused by multiple types of bacteria are tough to treat. For example, co-infections with Staphylococcus aureus and Pseudomonas aeruginosa are so difficult to cure they may persist for years in humans and cause serious illness. But when these two types of bacteria are grown together in the laboratory, P. aeruginosa kills off all the S. aureus. Learning why these two types of bacteria can coexist in people but not in the laboratory may lead to new treatments to clear infections. It may also help scientists grow beneficial bacteria mixes that break down pollution or produce biofuels. Pajon and Fortoul et al. show that interactions between bacterial metabolism and growth rate determine whether S. aureus and P. aeruginosa coexist. In the experiments, they grew both types of bacteria in different environments with different food sources. They measured their growth and metabolism and how many bacteria of each species survived over time. Then, they used their data to develop a mathematical model and tested its predictions in the laboratory again. The type of bacteria that had more energy also grew faster and outcompeted the other species. Measuring the growth rate of the two species allowed the scientists to predict which one would win out and what the tipping point would be. Physically disrupting the mix of bacteria disrupted this relationship. These results may help explain what allows these bacteria to coexist in some settings but not others. It may enable scientists to develop new ways to treat infections with P. aeruginosa and S. aureus that work by manipulating growth in the two species. Bacterial growth and metabolism are known to drive antibacterial resistance. Studies in mice using drugs or other therapies to manipulate growth and metabolism may help scientists thwart these resistance mechanisms. The results may also help scientists design and grow beneficial multispecies bacteria communities.

Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States.

Powassan virus is an emerging tick-borne virus of concern for public health, but very little is known about its transmission patterns and ecology. Here, we expanded the genomic dataset by sequencing 279 Powassan viruses isolated from Ixodes scapularis ticks from the northeastern United States. Our phylogeographic reconstructions revealed that Powassan virus lineage II was likely introduced or emerged from a relict population in the Northeast between 1940 and 1975. Sequences strongly clustered by sampling location, suggesting a highly focal geographical distribution. Our analyses further indicated that Powassan virus lineage II emerged in the northeastern United States mostly following a south-to-north pattern, with a weighted lineage dispersal velocity of ~3 km/y. Since the emergence in the Northeast, we found an overall increase in the effective population size of Powassan virus lineage II, but with growth stagnating during recent years. The cascading effect of population expansion of white-tailed deer and I. scapularis populations likely facilitated the emergence of Powassan virus in the northeastern United States.

Review of Continuing Medical Education in Tick-Borne Disease for Front-Line Providers.

Introduction: Considering increasing rates of tick-borne diseases (TBDs) in the United States, we investigated the scope of continuing medical education (CME) available to physicians on these infections. Methods: We surveyed online medical board and society databases serving front-line primary and emergency/urgent care providers for the availability of TBD-specific CME between March 2022 and June 2022. We recorded and analyzed opportunity title, author, web address, publication year, learning objectives, CME credit values, and CME credit type. Results: We identified 70 opportunities across seven databases. Thirty-seven opportunities focused on Lyme disease; 17 covered nine non-Lyme TBDs, and 16 covered general topics on TBDs. Most activities were hosted through family medicine and internal medicine specialty databases. Conclusion: These findings suggest limited availability of continuing education for multiple life-threatening TBDs of increasing importance in the United States. Increasing the availability of CME materials covering the broad scope of TBDs in targeted specialty areas is essential for increased content exposure and a necessary step to ensure our clinical workforce is adequately prepared to address this growing public health threat.

Phylodynamics of deer tick virus in North America.

The burden of ticks and the pathogens they carry is increasing worldwide. Powassan virus (POWV; Flaviviridae: Flavivirus), the only known North American tick-borne flavivirus, is of particular concern due to rising cases and the severe morbidity of POWV encephalitis. Here, we use a multifaceted approach to evaluate the emergence of the II POWV lineage, known as deer tick virus (DTV), in parts of North America where human cases occur. We detected DTV-positive ticks from eight of twenty locations in the Northeast USA with an average infection rate of 1.4 per cent. High-depth, whole-genome sequencing of eighty-four POWV and DTV samples allowed us to assess geographic and temporal phylodynamics. We observed both stable infection in the Northeast USA and patterns of geographic dispersal within and between regions. A Bayesian skyline analysis demonstrated DTV population expansion over the last 50 years. This is concordant with the documented expansion of Ixodes scapularis tick populations and suggests an increasing risk of human exposure as the vector spreads. Finally, we isolated sixteen novel viruses in cell culture and demonstrated limited genetic change after passage, a valuable resource for future studies investigating this emerging virus.

Disturbing the Spatial Organization of Biofilm Communities Affects Expression of agr-Regulated Virulence Factors in Staphylococcus aureus.

Staphylococcus aureus uses quorum sensing and nutrient availability to control the expression of agr-regulated virulence factors. Quorum sensing is mediated by autoinducing peptide (AIP), which at a high concentration reduces expression of surface attachment proteins (coa, fnbpA) and increases expression of exotoxins (lukS) and proteases (splA). Nutrient availability can be sensed through the saeS/saeR system. Low nutrients increase expression of saeR, which augments expression of coa and fnbpA, distinct from the activity of AIP. The formation of spatial structure, such as biofilms, can alter quorum sensing and nutrient acquisition. In natural environments, biofilms encounter forces that may alter their spatial structure. These forces may impact quorum sensing and/or nutrient acquisition and thus affect the expression of agr-regulated virulence factors. However, this has not been studied. We show that periodically disturbing biofilms composed of S. aureus using a physical force affected the expression of agr-regulated virulence factors. In nutrient-poor environments, disturbance increased the expression of coa, fnbpA, lukS, and splA. Disturbance in a nutrient-rich environment at low or high disturbance amplitudes moderately reduced expression of coa and fnbpA but increased expression of lukS and splA. Interestingly, at an intermediate amplitude, the overall expression of agr-regulated virulence factors was the lowest; expression of lukS and splA remained unchanged relative to an undisturbed biofilm, while expression of coa and fnbpA significantly decreased. We hypothesize that these changes are a result of disturbance-driven changes in access to AIP and nutrients. Our results may allow the identification of environments where virulence is enhanced, or reduced, owing to a disturbance. IMPORTANCE Bacteria, such as Staphylococcus aureus, integrate signals from the environment to regulate genes encoding virulence factors. These signals include those produced by quorum-sensing systems and nutrient availability. We show that disturbing the spatial organization of S. aureus populations can lead to changes in the expression of virulence factors, likely by altering the ways in which S. aureus detects these signals. Our work may allow us to identify environments that increase or reduce the expression of virulence factors in S. aureus.

Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment.

Conjugative plasmids often encode antibiotic resistance genes that provide selective advantages to their bacterial hosts during antibiotic treatment. Previous studies have predominantly considered these established genes as the primary benefit of antibiotic-mediated plasmid dissemination. However, many genes involved in cellular metabolic processes may also protect against antibiotic treatment and provide selective advantages. Despite the diversity of such metabolic genes and their potential ecological impact, their plasmid-borne prevalence, co-occurrence with canonical antibiotic resistance genes, and phenotypic effects remain widely understudied. To address this gap, we focused on Escherichia coli, which can often act as a pathogen, and is known to spread antibiotic resistance genes via conjugation. We characterized the presence of metabolic genes on 1,775 transferrable plasmids and compared their distribution to that of known antibiotic resistance genes. We found high abundance of genes involved in cellular metabolism and stress response. Several of these genes demonstrated statistically significant associations or disassociations with known antibiotic resistance genes at the strain level, indicating that each gene type may impact the spread of the other across hosts. Indeed, in vitro characterization of 13 statistically relevant metabolic genes confirmed that their phenotypic impact on antibiotic susceptibility was largely consistent with in situ relationships. These results emphasize the ecological importance of metabolic genes on conjugal plasmids, and that selection dynamics of E. coli pathogens arises as a complex consequence of both canonical mechanisms and their interactions with metabolic pathways.

Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics.

Understanding the mechanisms by which populations of bacteria resist antibiotics has implications in evolution, microbial ecology, and public health. The inoculum effect (IE), where antibiotic efficacy declines as the density of a bacterial population increases, has been observed for multiple bacterial species and antibiotics. Several mechanisms to account for IE have been proposed, but most lack experimental evidence or cannot explain IE for multiple antibiotics. We show that growth productivity, the combined effect of growth and metabolism, can account for IE for multiple bactericidal antibiotics and bacterial species. Guided by flux balance analysis and whole-genome modeling, we show that the carbon source supplied in the growth medium determines growth productivity. If growth productivity is sufficiently high, IE is eliminated. Our results may lead to approaches to reduce IE in the clinic, help standardize the analysis of antibiotics, and further our understanding of how bacteria evolve resistance.

Jamestown Canyon Virus in Collected Mosquitoes, Maine, United States, 2017-2019.

Jamestown Canyon virus (JCV) is a mosquito-borne arbovirus that circulates in North America. We detected JCV in 4 pools of mosquitoes collected from midcoastal Maine, USA, during 2017-2019. Phylogenetic analysis of a JCV sequence obtained from Aedes cantator mosquitoes clustered within clade A, which also circulates in Connecticut, USA.

First and Second Sound in a Compressible 3D Bose Fluid.

The two-fluid model is fundamental for the description of superfluidity. In the nearly incompressible liquid regime, it successfully describes first and second sound, corresponding, respectively, to density and entropy waves, in both liquid helium and unitary Fermi gases. Here, we study the two sounds in the opposite regime of a highly compressible fluid, using an ultracold ^{39}K Bose gas in a three-dimensional box trap. We excite the longest-wavelength mode of our homogeneous gas, and observe two distinct resonant oscillations below the critical temperature, of which only one persists above it. In a microscopic mode-structure analysis, we find agreement with the hydrodynamic theory, where first and second sound involve density oscillations dominated by, respectively, thermal and condensed atoms. Varying the interaction strength, we explore the crossover from hydrodynamic to collisionless behavior in a normal gas.

Frequency and Geographic Distribution of Borrelia miyamotoi, Borrelia burgdorferi, and Babesia microti Infections in New England Residents.

BACKGROUND: Borrelia miyamotoi is a relapsing fever spirochete that relatively recently has been reported to infect humans. It causes an acute undifferentiated febrile illness that can include meningoencephalitis and relapsing fever. Like Borrelia burgdorferi, it is transmitted by Ixodes scapularis ticks in the northeastern United States and by Ixodes pacificus ticks in the western United States. Despite reports of clinical cases from North America, Europe, and Asia, the prevalence, geographic range, and pattern of expansion of human B. miyamotoi infection are uncertain. To better understand these characteristics of B. miyamotoi in relation to other tickborne infections, we carried out a cross-sectional seroprevalence study across New England that surveyed B. miyamotoi, B. burgdorferi, and Babesia microti infections. METHODS: We measured specific antibodies against B. miyamotoi, B. burgdorferi, and B. microti among individuals living in 5 New England states in 2018. RESULTS: Analysis of 1153 serum samples collected at 11 catchment sites showed that the average seroprevalence for B. miyamotoi was 2.8% (range, 0.6%-5.2%), which was less than that of B. burgdorferi (11.0%; range, 6.8%-15.6%) and B. microti (10.0%; range, 6.5%-13.6%). Antibody screening within county residence in New England showed varying levels of seroprevalence for these pathogens but did not reveal a vectoral geographical pattern of distribution. CONCLUSIONS: Human infections caused by B. miyamotoi, B. burgdorferi, and B. microti are widespread with varying prevalence throughout New England.