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Background: Gene modified dendritic cells (DC) are able to modulate DC functions and induce therapeutic immunity or tolerance in an antigen-specific manner. Among the different DC subsets, plasmacytoid DC (pDC) are well known for their ability to recognize and respond to a variety of viruses by secreting high levels of type I interferon.Methods: We analyzed here, the transduction efficiency of a pDC cell line, GEN2.2, and of pDC derived from CD34+ progenitors, using lentiviral vectors (LV) pseudotyped with different envelope glycoproteins such as the vesicular stomatitis virus envelope (VSVG), the gibbon ape leukaemia virus envelope (GaLV) or the feline endogenous virus envelope (RD114). At the same time, we evaluated transgene expression (E-GFP reporter gene) under the control of different promoters.Results: We found that efficient gene transfer into pDC can be achieved with VSVG-pseudotyped lentiviral vectors (LV) under the control of phoshoglycerate kinase (PGK) and elongation factor-1 (EF1alpha) promoters (28% to 90% of E-GFP+ cells, respectively) in the absence of phenotypic and functional maturation. Surprisingly, promoters (desmin or synthetic C5-12) described as muscle-specific and which drive gene expression in single strand AAV vectors in gene therapy protocols were very highly active in pDC using VSVG-LV.Conclusion: Taken together, our results indicate that LV vectors can serve to design pDC-based vaccines in humans, and they are also useful in vitro to evaluate the immunogenicity of the vector preparations, and the specificity and safety of given promoters used in gene therapy protocols. [ABSTRACT FROM AUTHOR]

As interest in animal personality research grows, methodologies for quantifying consistent among-individual differences in behaviour are expanding. Two of the most common methods for quantifying animal personality are standardized behavioural assays and focal animal sampling. We evaluated whether assays and focals provided similar animal personality measures in a wild population of free-ranging North American red squirrels, Tamiasciurus hudsonicus , by comparing the among-individual correlations of traits between methods. Assays described two behavioural axes—one associated with movement behaviours and another associated with antagonistic behaviours towards conspecifics. Focals described two additional behavioural axes—one associated with movement and territorial behaviours, and another associated with the trade-off between vigilant and feeding behaviours. Although we found evidence of high trait repeatability for behavioural axes measured with assays, both focal behavioural axes had low trait repeatability regardless of whether among-individual differences in the social environment were controlled for (i.e. to account for 'pseudopersonality'). We also found no among-individual correlations between assay and focal behavioural axes. The lack of correlation between methods may be because the dominant axes of variation differ between methods or because of the low trait repeatability of focals due to high behavioural plasticity. Given this, we conclude that assays will likely remain the mainstay for measuring consistent among-individual differences in behaviour given their ability to standardize for environmental conditions. • We evaluated whether assay and focal observations measure similar behavioural axes. • Assays captured behaviours associated with movement and antagonistic behaviour. • Focals captured behaviours associated with territoriality and vigilance/feeding. • We found no among-individual correlations between methodologies. • Assays remain the mainstay for measuring personality by controlling for environment. [ABSTRACT FROM AUTHOR]

Few studies have applied NGS methods to investigate the microbiome of vertebrates in their natural environment and in freshwater fishes in particularly. Here, we used pyrosequencing of the 16S gene rRNA to (i) test for differences in kidney bacterial communities (i.e. microbiota) of dwarf and normal whitefish found as sympatric pairs, (ii) test the hypothesis of higher bacterial diversity in normal compared with dwarf whitefish and (iii) test for the occurrence of parallelism with the presence and composition of bacterial communities across species pairs inhabiting different lakes. The kidney microbiota of 253 dwarf and normal whitefish from five lakes was analysed combining a double-nested PCR approach with 454 pyrosequencing. Bacteria were detected in 52.6% of the analysed whitefish. There was no overall significant difference among lakes and forms, although the lake × form interaction was found significant. We identified 579 bacterial genera, which is substantially more than previous descriptions using less sensitive techniques of fish bacterial diversity in kidney, pathogenic or not. Ten of these genera contained eighteen pathogenic species. Differences in bacteria composition between whitefish forms were not parallel among lakes. In accordance with the higher diversity of prey types, normal whitefish kidney tissue consistently had a more diverse bacterial community and this pattern was parallel among lakes. These results add to building evidence from previous studies on this system that the adaptive divergence of dwarf, and normal whitefish has been driven by both parallel and nonparallel ecological conditions across lakes. [ABSTRACT FROM AUTHOR]

Understanding the factors that drive species distributions is emerging as an important tool in wildlife management, under unprecedented changes in species ranges. While invasion ecologists have long studied the impact of human land use on species' distributions, and models developed more recently to explain changes in species range boundaries have been largely parameterized by climate variables, few authors have considered climate and land-use factors together to explain species distribution. The purpose of this study was to test two main competing hypotheses involving human land use and climate effects on white-tailed deer ( Odocoileus virginianus (Zimmermann, 1780)) distribution, which has expanded into the boreal ecosystem in recent decades. Using a species distribution modeling approach with data from boreal Alberta, we found that climate, as measured by an index of winter severity, was the most important individual factor determining current white-tailed deer distribution in boreal Alberta. Human land use (as measured by total land-use footprint) acted to substantially increase white-tailed deer presence but only in areas with more severe winter conditions. We use our findings to recommend where limiting or reclaiming the industrial footprint may be most beneficial to limiting white-tailed deer distribution. [ABSTRACT FROM AUTHOR]

By regulating successional dynamics in Canada's boreal forest, fires can affect the distribution of the Threatened woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)). Caribou tend to avoid areas burned within the last 40 years; however, few studies have compared pre-fire and post-fire caribou observations. In this study, we used caribou GPS locations from the Boreal Shield of Saskatchewan, Canada, to assess the short-term response of caribou to areas that burned while they were collared (hereafter recent burns). We used a "before–after, control–impact" design to compare the overlap of pre-fire and post-fire seasonal home ranges to the overlap of year-to-year seasonal home ranges. Caribou rarely encountered recent burns and when they did, they adjusted their space use in variable and complex ways that were largely indistinguishable from regular, interannual variation. Caribou tended to reduce use of recent burns in summer–autumn and winter, but not during the calving season, in some cases shifting their home range to incorporate more burned habitat. We conclude that recently burned areas (<5 years) may provide habitat value to woodland caribou, particularly during the calving season, requiring a more flexible approach to interpret fire in habitat management strategies. [ABSTRACT FROM AUTHOR]

Animals switch between inactive and active states, simultaneously impacting their energy intake, energy expenditure and predation risk, and collectively defining how they engage with environmental variation and trophic interactions. We assess daily activity responses to long‐term variation in temperature, resources and mating opportunities to examine whether individuals choose to be active or inactive according to an optimisation of the relative energetic and reproductive gains each state offers. We show that this simplified behavioural decision approach predicts most activity variation (R2 = 0.83) expressed by free‐ranging red squirrels over 4 years, as quantified through accelerometer recordings (489 deployments; 5066 squirrel‐days). Recognising activity as a determinant of energetic status, the predictability of activity variation aggregated at a daily scale, and the clear signal that behaviour is environmentally forced through optimisation of gain, provides an integrated approach to examine behavioural variation as an intermediary between environmental variation and energetic, life‐history and ecological outcomes. [ABSTRACT FROM AUTHOR]

Natural disturbance plays a key role in shaping community dynamics. Within Canadian boreal forests, the dominant form of natural disturbance is fire, and its effects are thought to influence the dynamics between moose (Alces alces (Linnaeus, 1758)) and the boreal ecotype of woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)). Boreal caribou are considered "threatened" and population declines are attributed, at least in part, to disturbance-mediated apparent competition (DMAC) with moose. Here, we tested a primary prediction of the DMAC hypothesis: that moose respond positively to burns within and adjacent to the caribou range. We assessed moose selection for ≤25-year-old burns (when selection is predicted to be strongest) at multiple spatial scales and evaluated whether moose density was correlated with the extent of ≤40-year-old burns (a time frame predicted to negatively affect caribou). Against expectation, moose showed avoidance and low use of ≤25-year-old burns at all scales, regardless of burn age, season, and type of land cover burned. These findings mirrored the demographic response, as we found no correlation between ≤40-year-old burns and moose density. By contradicting the prevailing hypothesis linking fires to caribou population declines, our results highlight the need to understand regional variation in disturbance impacts on caribou populations. [ABSTRACT FROM AUTHOR]

Recently, following import by travel and migration, epidemic community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has caused nosocomial outbreaks in Europe, sometimes with a fatal outcome. We describe clinico-epidemiological characteristics of CA-MRSA detected by the European Network for the Surveillance of imported S. aureus (www.staphtrav.eu) from May 2011 to November 2016. Sentinel surveillance at 13 travel clinics enrolling patients with travel-associated skin and soft-tissue infection (SSTI) and analysing lesion and nose swabs at one central laboratory. A total of 564 independent case-patients with SSTI were enrolled and had 374 (67%) S. aureus -positive lesions, of which 14% (51/374) were MRSA. The majority of CA-MRSA isolates from SSTI were Panton–Valentine leucocidin (PVL) -positive (43/51, 84%). The risk of methicillin-resistance in imported S. aureus varied by travel region (p <0.001) and was highest in Latin America (16/57, 28%, 95% CI 17.0–41.5) and lowest in Sub-Saharan Africa (4/121, 3%, 95% CI 0.9–8.3). Major epidemic clones (USA300 / USA300 Latin-American Variant, Bengal Bay, South Pacific) accounted for more than one-third (19/51, 37%) of CA-MRSA imports. CA-MRSA SSTI in returnees was complicated (31/51 multiple lesions, 61%; 22/50 recurrences, 44%), led to health-care contact (22/51 surgical drainage, 43%; 7/50 hospitalization, 14%), was transmissible (13/47 reported similar SSTI in non-travelling contacts, 28%), and associated with S. aureus nasal colonization (28 of 51 CA-MRSA cases, 55%; 24 of 28 colonized with identical spa -type in nose and lesion, 85%). Travel-associated CA-MRSA SSTI is a transmissible condition that leads to medical consultations and colonization of the infected host. [ABSTRACT FROM AUTHOR]

White spruce ( Picea glauca (Moench) Voss) cone crops were measured at five regional centers in southern and central Yukon for 30 years at one site from 1986 to 2015 and at four other sites during 9 to 11 years to select the best climatic model that uses cues from growing season temperature and rainfall to predict the size of cone crops. We evaluated six climatic models that use summer temperature and rainfall of years t - 1 and t - 2 to predict cone crops in year t. July temperatures provided the best predictors of white spruce cone crops, and no rainfall variable was related to the size of cone crops. We explored three variants of July temperatures: mean temperature, degree-days > 5 °C, and maximum temperatures. For each of these, we used the Δ T model that uses the difference in the July temperature measures of years t - 1 and t - 2. We compared the resulting six models with corrected Akaike's information criterion (AICc) to determine their relative predictive performance. The best model combined Δ T measures of degree-days > 5 °C and the four highest daily maximum July temperatures with R2 = 0.65. By comparison, the Δ T model involving only mean July temperatures was less successful ( R2 = 0.49). There was good regional synchrony ( rp = 0.7 to 0.8) in high cone crops over southern and central Yukon during 1986 to 2015. [ABSTRACT FROM AUTHOR]

Most empirical attempts to explain the evolution of parental care have focused on its costs and benefits (i.e. fitness consequences). In contrast, few investigations have been made of the other necessary prerequisite for evolutionary change, inheritance. Here, we examine the fitness consequences and heritability ( h 2) of a post-weaning parental care behaviour (territory bequeathal) in a wild population of North American red squirrels. Each year, a subset (average across all years = 19%) of reproductive females bequeathed their territory to a dependent offspring. Bequeathing females experienced higher annual reproductive success and did not suffer a survival cost to themselves relative to those females retaining their territory. Bequeathing females thus realized higher relative annual fitness [ ω = 1.18 ± 0.03 ( SE)] than nonbequeathing females [ ω = 0.96 ± 0.02 ( SE)]. Additive genetic influences on bequeathal behaviour, however, were not significantly different from 0 ( h 2 = 1.9 × 10−3; 95% highest posterior density interval = 3.04 × 10−8 to 0.37) and, in fact, bequeathal behaviour was not significantly repeatable ( R = 2.0 × 10−3; 95% HPD interval =0-0.27). In contrast, directional environmental influences were apparent. Females were more likely to bequeath in years following low food abundance and when food availability in the upcoming autumn was high. Despite an evident fitness benefit, a lack of heritable genetic variance will constrain evolution of this trait. [ABSTRACT FROM AUTHOR]

Estimation of demographic trends from vital rates provides a powerful means to estimate population trends in cryptic or difficult to study species such as woodland caribou ( Rangifer tarandus caribou (Gmelin, 1788)). Using such methods, Hervieux et al. (2013; Can. J. Zool. 92(12): 872-882) recently showed 11 of 14 woodland caribou populations in Alberta were declining at ∼8%/year following up to 18 years of monitoring. Harron (2015; Can. J. Zool. 93(2): 149-150) critiques our original study, claiming that negative biases in our demographic monitoring exaggerate our conclusions of widespread caribou declines. Here, we systematically review each of Harron's claims of bias, rejecting each of his claims upon careful review of the mechanisms by which his purported claims would manifest in our population trend estimation. Therefore, we conclude that Harron's scientific critique was superficial and misleading. Delays in conservation actions raised by Harron's critique risk diminishing opportunities to conserve and recover this federally and provincially protected species. [ABSTRACT FROM AUTHOR]

Nowhere across Canada is the continued persistence of woodland caribou ( Rangifer tarandus caribou (Gmelin, 1788)) more uncertain than in Alberta due to widespread industrial development. A recent Government of Canada critical habitat review determined that habitat conditions within all Alberta boreal ecotype caribou ranges are unlikely or very unlikely to allow for self-sustaining caribou populations. This habitat-based assessment was based only indirectly on empirical population trends. Here, we estimated empirical population trend and growth rate ( λ) for 13 of Alberta's 16 remaining woodland caribou populations (plus one adjacent population from Saskatchewan) from 1994 to 2012 using demographic monitoring of adult female survival and calf recruitment. We captured and radio-collared a total of 1337 adult female caribou in 14 populations and estimated the mean annual adult female survival across all populations as 0.851. We conducted 158 late-winter calf recruitment surveys across the 14 populations classifying 20 872 caribou and estimated mean recruitment of 0.154 calves/cow (i.e., 0.077 female calves/cow). We then combined annual estimates of adult female survival and female calf recruitment within each population in a simple age-structured population model to estimate population trend. Annual population growth rate across caribou populations averaged 0.918, and was significantly declining, λ < 1.0, for 10 of the 14 caribou populations. Our results confirm that woodland caribou are declining rapidly (with a realized decline of approximately 50% every 8 years) across Alberta, and support conclusions from previous habitat-based assessments that the population viability of caribou is currently compromised, supporting development and implementation of recovery actions to reverse trends. [ABSTRACT FROM AUTHOR]

Consistent individual differences in behaviour, and behavioural correlations within and across contexts, are referred to as animal personalities. These patterns of variation have been identified in many animal taxa and are likely to have important ecological and evolutionary consequences. Despite their importance, genetic and environmental sources of variation in personalities have rarely been characterized in wild populations. We used a Bayesian animal model approach to estimate genetic parameters for aggression, activity and docility in North American red squirrels (Tamiasciurus hudsonicus). We found support for low heritabilities (0.08-0.12), and cohort effects (0.07-0.09), as well as low to moderate maternal effects (0.07-0.15) and permanent environmental effects (0.08-0.16). Finally, we found evidence of a substantial positive genetic correlation (0.68) and maternal effects correlation (0.58) between activity and aggression providing evidence of genetically based behavioural correlations in red squirrels. These results provide evidence for the presence of heritable variation in red squirrel behaviour, but also emphasize the role of other sources of variation, including maternal effects, in shaping patterns of variation and covariation in behavioural traits. [ABSTRACT FROM AUTHOR]

White spruce ( (Moench) Voss) cone crops were measured from 1986 to 2011 in the Kluane region of southwestern Yukon to test the hypothesis that the size of cone crops could be predicted from spring and summer temperature and rainfall of years t, t - 1, and t - 2 . We counted cones in the top 3 m of an average of 700 white spruce trees each year spread over 3-14 sites along 210 km of the Alaska Highway and the Haines Highway. We tested the conventional explanation for white spruce cone crops that implicates summer temperatures and rainfall in years t and t - 1 and rejected it, since it explained very little of the variation in our 26 years of data. We used exploratory data analysis with robust multiple regressions coupled with Akaike's information criterion corrected (AICc) analysis to determine the best statistical model to predict the size of cone crops. We could statistically explain 54% of the variation in cone crops from July and August temperatures of years t - 1 and t - 2 and May precipitation of year t - 2. There was no indication of a periodicity in cone crops, and years of large cone crops were synchronous over the Kluane region with few exceptions. This is the first quantitative model developed for the prediction of white spruce cone crops in the Canadian boreal forest and has the surprising result that weather conditions 2 years prior to the cone crop are the most significant predictors. [ABSTRACT FROM AUTHOR]

The hypothesis that cold air temperatures (Ta) constrain the metabolic diversity of high-latitude endotherms is based on the observation among birds and mammals that mean field metabolic rate (FMR) increases, whereas the variability of FMR decreases, from the warm tropics to the cold poles. However, there is a paucity of FMR measurements from above 60° latitude and below 0 °C. We measured the daily energy expenditure of a high-latitude population of free-ranging snowshoe hares (Lepus americanus Erxleben, 1777) in Yukon, Canada, in winter (Ta-mean = -16.4 °C) and in autumn (Ta-mean = 0.5 °C). Doubly labelled water measures of FMR were approximately 20% lower in winter than in autumn, and were a similar, low multiple of resting metabolic rate in both seasons (2.04 and 1.94, respectively). The mass-corrected FMR of snowshoe hares in winter was only half the value predicted by extrapolating the relationship between FMR and Ta > 0 to -16.4 °C. These results contribute to an emerging pattern of a reversal in the relationship between FMR and Ta in free-ranging mammals from negative above 0 °C to positive below 0 °C. We refer to the positive, low Ta portion of this relationship as the cold shoulder, and suggest that it may reflect the general necessity for free-ranging mammals to use behavioural and (or) physiological means to conserve energy during long winters when cold conditions coincide with resource scarcity. [ABSTRACT FROM AUTHOR]

Models of community organization involve variations of the top-down (predator control) or bottom-up (nutrient limitation) hypotheses. Verbal models, however, can be interpreted in different ways leading to confusion. Therefore, we predict from first principles the range of possible trophic level interactions, and define mathematically the instantaneous effects of experimental perturbations. Some of these interactions are logically and biologically unfeasible. The remaining set of 27 feasible models is based on an initial assumption, for simplicity, of linear interactions between trophic levels. Many more complex and non-linear models are logically feasible but, for parsimony, simple ones are tested first. We use an experiment in the boreal forest of Canada to test predictions of instantaneous changes to trophic levels and distinguish between competing models. Seven different perturbations systematically removed each trophic level or, for some levels, supplemented them. The predictions resulting from the perturbations were concerned with the direction of change in biomass in the other levels. The direct effects of each perturbation produced strong top-down and bottom-up changes in biomass. At both the vegetation and herbivore levels top-down was stronger than bottom-up despite some compensatory growth stimulated by herbivory. The combination of experiments produced results consistent with two-way (reciprocal) interactions at each level. Indirect effects on one or two levels removed from the perturbation were either very weak or undetectable. Top-down effects were strong when direct but attenuated quickly. Bottom-up effects were less strong but persisted as indirect effects to higher levels. Although the ‘pure reciprocal’ model best fits our results for the boreal forest system different models may apply to different ecosystems around the world. [ABSTRACT FROM AUTHOR]

• We present a model of apparent competition, parametrized using empirical data, to predict habitat restoration efficacy. • Habitat restoration has the potential to increase caribou densities by up to 2.51-fold. • Increases in caribou density can occur with minimal changes to wolf or moose density. • Incorporating the numerical feedback into simulations of foraging efficiency increased our understanding of the total response. • Simulated predator reductions increased caribou densities by more than twice the total response of restoration, suggesting restoration should be coupled with other direct management actions. Predator-prey dynamics are increasingly being modified by the alteration of natural habitats. Such alteration has led to increased predation rates and local extirpation of woodland caribou (Rangifer tarandus caribou) in western Canada. Linear features such as roads or seismic lines (narrow corridors used for petroleum exploration that are cleared of vegetation) increase predation rates on caribou by increasing wolf (Canis lupus) movement rates and by facilitating access into caribou habitat. Linear feature restoration is therefore hypothesised to help reverse caribou declines. However, with the high financial cost to restore approximately 350,000 km of seismic lines within western Canada's boreal forests, theoretical predictions can clarify the efficacy of such actions. We use a mathematical model based on coupled ordinary differential equations representing predator-prey dynamics to estimate equilibrium densities of caribou, moose (Alces alces) and wolves under various parameter scenarios. Changes in equilibrium density serve as a proxy for the expected effect of linear feature restoration on population densities. Our model captures dynamical feedbacks between caribou and wolf densities, and also includes moose, which are the wolf's primary prey species. With our best estimates of parameter values, caribou density increased 2.51-fold if all linear features were restored and 1.61-fold if only seismic lines were restored. As a comparison, simulated predator reductions increased caribou densities 3.92-fold, nearly twice the total response of linear feature restoration. The effect of restoration was increased if caribou group size was smaller, yet was less pronounced if carrying capacity for ungulates was higher. By varying the parameter values and fixing population densities, our approach allowed us to partition the caribou populations' response from restoration into the contributions of the various mechanisms and feedbacks. In particular, contrasting simulation results where wolf densities are kept fixed with those where they are free to respond to prey allowed us to disentangle the relative importance of wolf functional and numerical response. This novel approach indicates that most of the increase in caribou densities after restoration was due to reduced foraging efficiency of wolves, especially reduced habitat overlap. Overall, our results suggest that restoration could substantially benefit caribou populations, but only if all linear features are restored, which is far from realistic. Linear feature restoration alone may not lead to population recovery, and should therefore be coupled with other direct management actions to successfully recover caribou. [ABSTRACT FROM AUTHOR]

The discovery of tumor-associated antigens recognized by T lymphocytes opens the possibility of vaccinating cancer patients with defined antigens. However, one of the major limitation of peptide-based vaccines is the low immunogenicity of antigenic peptides. Interestingly, if these epitopes are directly delivered into the cytoplasm of antigen presenting cells, they can be efficiently presented via the direct MHC class I presentation pathway. To improve antigen entry, one promising approach is the use of cell penetrating peptides (CPPs). However, most studies use a covalent binding of the CPP with the antigen. In the present study, we focused on the C-terminal domain of Vpr which was previously demonstrated to efficiently deliver plasmid DNA into cells. We provide evidence that the peptides Vpr55-91 and Vpr55-82 possess the capacity of delivering proteins and epitopes into cell lines as well as into human primary dendritic cells, without the necessicity for a chemical linkage. Moreover, immunization of HLA-A2 transgenic mice with Vpr55-91 as the sole adjuvant is able to induce antigen-specific cytotoxic T lymphocytes against multiple tumor epitopes. [ABSTRACT FROM AUTHOR]

Competing Interests: DN received speaker honoraria from Shionogi and Cepheid outside the scope of this work. All other authors declared no conflicts of interest. The funding sources were not involved in the design, implementation or analysis of the study or in the writing of the decision to submit it for publication.

Introduction: Central nervous system infections pose significant health challenges, particularly in low- and middle-income countries, because of high morbidity and mortality rates. Rapid and accurate diagnosis is essential for effective treatment to prevent adverse outcomes. Traditional culture-based diagnostics are often slow and lack specificity. This study evaluates the BioFire FilmArray Meningitis/Encephalitis (FAME) Panel against standard diagnostics in Vietnam to assess its clinical impact and suitability for local epidemiology., Methods: We conducted a prospective study involving 330 patients with suspected central nervous system infections at 4 hospitals in northern Vietnam from July 2022 to April 2023. Cerebrospinal fluid samples were analyzed using routine culture methods and FAME. We compared pathogen detection rates and assessed the potential clinical impact of FAME results on patient management., Results: Of the 330 cerebrospinal fluid specimens, 64 (19%) were positive by either conventional diagnostics (n = 48) and/or FAME (n = 33). The agreement between FAME and conventional diagnostics was 87%. Key pathogens Mycobacterium tuberculosis (n = 7), Klebsiella pneumoniae (n = 5), Streptococcus suis (n = 5), Epstein-Barr virus (n = 3), Acinetobacter baumannii (n = 1), and Trichosporon asahii (n = 1) were not detected by FAME. Classical meningitis parameter clinical symptoms, altered glucose, protein, and pleocytosis were good predictors of FAME positivity, indicating their utility in optimizing local diagnostic algorithms., Conclusions: FAME complements traditional diagnostics by offering rapid and broad pathogen detection, crucial for timely and appropriate therapy. However, its effectiveness varies with local epidemiology, and it should not replace conventional methods entirely. Tailoring diagnostic panels to regional pathogen prevalence is recommended to enhance diagnostic accuracy and clinical outcomes in low- and middle-income countries., Competing Interests: Potential conflicts of interest. All authors: No reported conflicts., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

In Dickie et al. (2024), we contrasted the effects of climate and habitat alteration on white-tailed deer density, recognizing the role of both these factors. Barnas et al.'s (2024) critique raised concerns about data transformations, model overfitting, and inference methods, but our analysis demonstrates that these criticisms are either unfounded or align with our original conclusions. We reaffirm that while both climate and habitat alteration contribute to deer densities, management decisions cannot ignore the strong role of climate, which is only predicted to increase in coming decades., (© 2024 The Author(s). Global Change Biology published by John Wiley & Sons Ltd.)

Competing Interests: DN received speaker honoraria from Shionogi and Cepheid outside the scope of this work. DN and TPV are members of the PAN-ASEAN Coalition for Epidemic and Outbreak Preparedness (DAAD-PACE-UP Project ID: 57592343) and acknowledge their funding for this study. All other authors declare no conflicts of interest.

Purpose: To characterize the clinical relevance of S. saccharolyticus and to identify criteria to distinguish between infection and contamination., Methods: We retrospectively investigated clinical features of patients with S. saccharolyticus detection between June 2009 and July 2021. Based on six criteria, infection was considered likely for patients with a score from 3 to 6 points, infection was considered unlikely for patients with a score from 0 to 2 points. We performed group comparison and logistic regression to identify factors than are associated with likely infection. In addition, whole genome sequencing (WGS) of 22 isolates was performed., Results: Of 93 patients in total, 44 were assigned to the group "infection likely" and 49 to the group "infection unlikely". Multiple regression analysis revealed "maximum body temperature during hospital stay" to have the strongest predictive effect on likely infection (adjusted odds ratio 4.40, 95% confidence interval 2.07-9.23). WGS revealed two different clades. Compared to isolates from clade A, isolates from clade B were more frequently associated with implanted medical devices (3/10 vs. 9/12, p = 0.046) and a shorter time to positivity (TTP) (4.5 vs. 3, p = 0.016). Both clades did neither differ significantly in terms of causing a likely infection (clade A 7/10 vs. clade B 5/12, p = 0.23) nor in median length of hospital stay (28 vs. 15.5 days, p = 0.083) and length of stay at the ICU (21 vs. 3.5 days, p = 0.14)., Conclusion: These findings indicate that S. saccharolyticus can cause clinically relevant infections. Differentiation between infection and contamination remains challenging., (© 2024. The Author(s).)

Background: The rise of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) in low- and middle-income countries limits treatment options, leading to the frequent use of broad-spectrum antibiotics. Reducing time-to-result for a urinary infection can facilitate correct antibiotic treatment and support antimicrobial and diagnostic stewardship measures. This study compared two simplified enrichment methods for detecting CTX-M directly from urine specimens., Methods: Two enrichment methods, namely centrifugation of 2 mL urine and filtration of 1 mL urine using the DirecTool adaptor, were compared using 20 culture-positive urine samples (20 suspected ESBL-E and 20 non-ESBL-E). CTX-M production was detected using a lateral flow assay (LFA), NG-Test ® CTX-MMULTI. The presence of bla CTX-M genes was confirmed by whole-genome sequencing (WGS)., Results: The results of both enrichment methods were identical, with a sensitivity of 87.5% and a specificity of 100%. In 19/20 (95%) of the urine samples, the results of the CTX-M LFA were identical with the phenotypic confirmation and WGS. Both methods could detect ESBL-E bacteriuria with ≥10 4 cfu/mL. All ESBL-E-negative samples were identified accurately. Both enrichment methods yielded negative results in one ESBL-E-positive (CTX-M-15) sample despite phenotypic and genotypic confirmation of ESBL production. High leukocyte count (>500 cells/µL), the presence of boric acid or polymicrobial samples did not appear to impact the performance of both enrichment methods., Conclusions: Our study underscores the feasibility of directly detecting CTX-M in urine. Simplified enrichment methods, particularly with a filtration kit, enhance the assay's practicality, rendering it suitable for use in primary care, emergency departments or remote laboratories without sophisticated equipment., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Population and community ecology as a science are about 100 years old, and we discuss here our opinion of what approaches have progressed well and which point to possible future directions. The three major threads within population and community ecology are theoretical ecology, statistical tests and models, and experimental ecology. We suggest that our major objective is to understand what factors determine the distribution and abundance of organisms within populations and communities, and we evaluate these threads against this major objective. Theoretical ecology is elegant and compelling and has laid the groundwork for achieving our overall objectives with useful simple models. Statistics and statistical models have contributed informative methods to analyze quantitatively our understanding of distribution and abundance for future research. Population ecology is difficult to carry out in the field, even though we may have all the statistical methods and models needed to achieve results. Community ecology is growing rapidly with much description but less understanding of why changes occur. Biodiversity science cuts across all these subdivisions but rarely digs into the necessary population and community science that might solve conservation problems. Climate change affects all aspects of ecology but to assume that everything in population and community ecology is driven by climate change is oversimplified. We make recommendations on how to advance the field with advice for present and future generations of population and community ecologists., (© 2024 The Author(s). Integrative Zoology published by International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.)

The disease burden of Streptococcus pyogenes is particularly high in low- and middle-income countries. However, data on the molecular epidemiology of S. pyogenes in such regions, especially sub-Saharan Africa, are scarce. To address this, whole-genome sequencing (WGS) of S. pyogenes from Gabon was performed to identify transmission clusters and provide valuable genomic data for public repositories. A total of 76 S . pyogenes isolates from 73 patients, collected between September 2012 and January 2013, were characterized by short-read whole-genome sequencing. The predominant emm types were emm 58.0, emm 81.2 and emm 223.0 with 9.2% (7 of 76), 7.9% (6 of 76), and 6.6% (5 of 76), respectively. Single-nucleotide polymorphism analysis revealed 16 putative transmission clusters. Four of these were household transmissions. Four antimicrobial genes ( lmrP , tetM , tetL , and thfT ) were found in the S. pyogenes isolates from this study. All strains carried lmrP . Of the 76 isolates, 64 (84.2%) carried at least one tetracycline resistance gene ( tetM or tetL ). Comparisons with other publicly available African genomic data revealed a significant correlation between geographical location and genetic diversity of S. pyogenes , with Gabonese strains showing similarities to those from Kenya and certain Oceanian regions. Our study showed that transmission of S. pyogenes can occur at the community/household level and that high-resolution molecular typing is needed to monitor changes in circulating clones and to detect community outbreaks. Advocacy for the adoption of WGS for comprehensive molecular characterization of S. pyogenes and data sharing through public repositories should be encouraged to understand the molecular epidemiology and evolutionary trajectory of S. pyogenes in sub-Saharan Africa., Importance: The study conducted in Gabon underscores the critical importance of addressing the limited knowledge of the molecular epidemiology of Streptococcus pyogenes in low- and middle-income countries, particularly sub-Saharan Africa. Our molecular analysis identified predominant emm types and unveiled 16 putative transmission clusters, four involving household transmissions. Furthermore, the study revealed a correlation between geographical location and genetic diversity, emphasizing the necessity for a comprehensive understanding of the molecular epidemiology and evolutionary trajectory of S. pyogenes in various regions. The call for advocacy in adopting whole-genome sequencing for molecular characterization and data sharing through public repositories is crucial for advancing our knowledge and implementing effective strategies to combat the spread of S. pyogenes in sub-Saharan Africa., Competing Interests: The authors declare no conflict of interest.