Multi-habitat landscapes are more diverse and stable with improved function.

Conservation, restoration and land management are increasingly implemented at landscape scales1,2. However, because species interaction data are typically habitat- and/or guild-specific, exactly how those interactions connect habitats and affect the stability and function of communities at landscape scales remains poorly understood. We combine multi-guild species interaction data (plant-pollinator and three plant-herbivore-parasitoid communities, collected from landscapes with one, two or three habitats), a field experiment and a modelling approach to show that multi-habitat landscapes support higher species and interaction evenness, more complementary species interactions and more consistent robustness to species loss. These emergent network properties drive improved pollination success in landscapes with more habitats and are not explained by simply summing component habitat webs. Linking landscape composition, through community structure, to ecosystem function, highlights mechanisms by which several contiguous habitats can support landscape-scale ecosystem services.

Comparative effects of calcitriol and calcimimetic on bone health in renal insufficiency.

Calcitriol and calcimimetics are used to treat hyperparathyroidism secondary to chronic kidney disease (CKD). Calcitriol administration and the subsequent increase in serum calcium concentration decrease parathyroid hormone (PTH) levels, which should reduce bone remodeling. We have previously reported that, when maintaining a given concentration of PTH, the addition of calcimimetics is associated with an increased bone cell activity. Whether calcitriol administration affects bone cell activity while PTH is maintained constant should be evaluated in an animal model of renal osteodystrophy. The aim of the present study was to compare in CKD PTH-clamped rats the bone effects of calcitriol and calcimimetic administration. The results show that the administration of calcitriol and calcimimetic at doses that induced a similar reduction in PTH secretion produced dissimilar effects on osteoblast activity in 5/6 nephrectomized (Nx) rats with secondary hyperparathyroidism and in Nx rats with clamped PTH. Remarkably, in both rat models, the administration of calcitriol decreased osteoblastic activity, whereas calcimimetic increased bone cell activity. In vitro, calcitriol supplementation inhibited nuclear translocation of ß-catenin and reduced proliferation, osteogenesis, and mineralization in mesenchymal stem cells differentiated into osteoblasts. In conclusion, besides the action of calcitriol and calcimimetics at parathyroid level, these treatments have specific effects on bone cells that are independent of the PTH level.

Cognitive Impairment Related to Chronic Kidney Disease Is Associated with a Decreased Abundance of Membrane-Bound Klotho in the Cerebral Cortex.

Cognitive impairment (CI) is a complication of chronic kidney disease (CKD) that is frequently observed among patients. The aim of this study was to evaluate the potential crosstalk between changes in cognitive function and the levels of Klotho in the brain cortex in an experimental model of CKD. To induce renal damage, Wistar rats received a diet containing 0.25% adenine for six weeks, while the control group was fed a standard diet. The animals underwent different tests for the assessment of cognitive function. At sacrifice, changes in the parameters of mineral metabolism and the expression of Klotho in the kidney and frontal cortex were evaluated. The animals with CKD exhibited impaired behavior in the cognitive tests in comparison with the rats with normal renal function. At sacrifice, CKD-associated mineral disorder was confirmed by the presence of the expected disturbances in the plasma phosphorus, PTH, and both intact and c-terminal FGF23, along with a reduced abundance of renal Klotho. Interestingly, a marked and significant decrease in Klotho was observed in the cerebral cortex of the animals with renal dysfunction. In sum, the loss in cerebral Klotho observed in experimental CKD may contribute to the cognitive dysfunction frequently observed among patients. Although further studies are required, Klotho might have a relevant role in the development of CKD-associated CI and represent a potential target in the management of this complication.

Variation in diversity-function relationships can be explained by species interactions.

Research Highlight: Wu, D., Xu, C., Wang, S., Zhang, L., & Kortsch, S. (2022). Why are biodiversity-ecosystem functioning relationships so elusive? Trophic interactions may amplify ecosystem function variability. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.13808. There is consensus that average trends of ecosystem functions increase with species diversity. However, large variations in ecosystem function (VEF) in systems with similar diversity levels are commonly observed, yet not understood. In this study, Wu et al. (2022) integrate empirical aquatic food webs with a multitrophic model to show that VEF generally shows a hump-shaped pattern along the species richness gradient. This pattern is related to changes in taxa composition across trophic levels-the proportion of consumer species relative to basal species-along the gradient of species richness. Thus, VEF dependence on species diversity is driven by both bottom-up and top-down control that regulate taxa composition and taxa dominance. These results are corroborated with an independent food web dataset from the Gulf of Riga. An important implication of this study is that biodiversity loss may not only reduce the mean levels of ecosystem functioning, but also increase unpredictability of functions by generating greater function variability.

What Is It like to Be a Brain Organoid? Phenomenal Consciousness in a Biological Neural Network.

It has been shown that three-dimensional self-assembled multicellular structures derived from human pluripotent stem cells show electrical activity similar to EEG. More recently, neurons were successfully embedded in digital game worlds. The biologically inspired neural network (BNN), expressing human cortical cells, was able to show internal modification and learn the task at hand (predicting the trajectory of a digital ball while moving a digital paddle). In other words, the system allowed to read motor information and write sensory data into cell cultures. In this article, we discuss Neural Correlates of Consciousness (NCC) theories, and their capacity to predict or even allow for consciousness in a BNN. We found that Information Integration Theory (IIT) is the only NCC that offers the possibility for a BNN to show consciousness, since the Φ value in the BNN is >0. In other words, the recording of real-time neural activity responding to environmental stimuli. IIT argues that any system capable of integrating information will have some degree of phenomenal consciousness. We argue that the pattern of activity appearing in the BNN, with increased density of sensory information leading to better performance, implies that the BNN could be conscious. This may have profound implications from a psychological, philosophical, and ethical perspective.

Enriched-biochar application increases broccoli nutritional and phytochemical content without detrimental effect on yield.

BACKGROUND: Soil fertility is a major concern during vegetable production. Conventional versus organic fertilization has been studied in order to conserve soil properties. While some reports point out an increase in food nutritional properties, the loss of crop yield under organic conditions continues to be a problem. Thus, an experiment with broccoli in the field was carried out, comparing crop management under conventional fertilization (CF) and two soil amendment treatments: manure pellet (M) and an enriched-biochar (EB) supplemented by an organic fertilizer (AND) applied alone (M + CF; EB+AND) or in combination (M + EB + AND). Crop yield and the nutritional properties in the flowering heads (mineral content, phenolic compounds and glucosinolates (GSLs)), were determined. RESULTS: Enriched-biochar and manure as a standalone amendment resulted in higher crop yield regarding CF, but not when they were applied in combination. The number of flowering heads with no-commercial characteristics was lower after enriched-biochar soil application. Finally, enriched-biochar treatment enhanced NO3 - , PO4 3- and SO4 2- levels in the flowering heads, and some of the ion contents can be associated with mineral changes in the soil after the biochar amendment. Also, the contents of phenolic compounds and indole GSLs were higher after enriched-biochar application compared with the other treatments, GSL increase being due to the higher percentage of sulfur in the plant rather that an adequate N/S ratio. CONCLUSION: Application of enriched-biochar amendment in the cultivation of broccoli is appropriate, since there are no losses of yield and an increase in nutritional compounds in the flowering heads. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Orthology and synteny analysis of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes.

BACKGROUND: Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses directly involve plasma membrane receptor proteins known as receptor-like kinases and receptor-like proteins. Evaluating the homology relations among RLK and RLP for seven legume species, and exploring their presence among synteny blocks allow an increased understanding of evolutionary relations, physical position, and chromosomal distribution in related species and their shared roles in stress responses. RESULTS: Typically, a high proportion of RLK and RLP legume proteins belong to orthologous clusters, which is confirmed in this study, where between 66 to 90% of the RLKs and RLPs per legume species were classified in orthologous clusters. One-third of the evaluated syntenic blocks had shared RLK/RLP genes among both legumes and non-legumes. Among the legumes, between 75 and 98% of the RLK/RLP were present in syntenic blocks. The distribution of chromosomal segments between Phaseolus vulgaris and Vigna unguiculata, two species that diverged ~ 8 mya, were highly similar. Among the RLK/RLP synteny clusters, seven experimentally validated resistance RLK/RLP genes were identified in syntenic blocks. The RLK resistant genes FLS2, BIR2, ERECTA, IOS1, and AtSERK1 from Arabidopsis and SLSERK1 from Solanum lycopersicum were present in different pairwise syntenic blocks among the legume species. Meanwhile, only the LYM1- RLP resistant gene from Arabidopsis shared a syntenic blocks with Glycine max. CONCLUSIONS: The orthology analysis of the RLK and RLP suggests a dynamic evolution in the legume family, with between 66 to 85% of RLK and 83 to 88% of RLP belonging to orthologous clusters among the species evaluated. In fact, for the 10-species comparison, a lower number of singleton proteins were reported among RLP compared to RLK, suggesting that RLP positions are more physically conserved compared to RLK. The identification of RLK and RLP genes among the synteny blocks in legumes revealed multiple highly conserved syntenic blocks on multiple chromosomes. Additionally, the analysis suggests that P. vulgaris is an appropriate anchor species for comparative genomics among legumes.

Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes.

BACKGROUND: In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are crucial in plant development and immunity. These plasma membrane receptors belong to large gene/protein families that are not easily classified computationally. This detailed analysis of these plasma membrane proteins brings a new source of information to the legume genetic, physiology and breeding research communities. RESULTS: A computational approach to identify and classify RLK and RLP proteins is presented. The strategy was evaluated using experimentally-validated RLK and RLP proteins and was determined to have a sensitivity of over 0.85, a specificity of 1.00, and a Matthews correlation coefficient of 0.91. The computational approach can be used to develop a detailed catalog of plasma membrane receptors (by type and domains) in several legume/crop species. The exclusive domains identified in legumes for RLKs are WaaY, APH Pkinase_C, LRR_2, and EGF, and for RLP are L-lectin LPRY and PAN_4. The RLK-nonRD and RLCK subclasses are also discovered by the methodology. In both classes, less than 20% of the total RLK predicted for each species belong to this class. Among the 10-species evaluated ~ 40% of the proteins in the kinome are RLKs. The exclusive legume domain combinations identified are B-Lectin/PR5K domains in G. max, M. truncatula, V. angularis, and V. unguiculata and a three-domain combination B-lectin/S-locus/WAK in C. cajan, M. truncatula, P. vulgaris, V. angularis. and V. unguiculata. CONCLUSIONS: The analysis suggests that about 2% of the proteins of each genome belong to the RLK family and less than 1% belong to RLP family. Domain diversity combinations are greater for RLKs compared with the RLP proteins and LRR domains, and the dual domain combination LRR/Malectin were the most frequent domain for both groups of plasma membrane receptors among legume and non-legume species. Legumes exclusively show Pkinase extracellular domains, and atypical domain combinations in RLK and RLP compared with the non-legumes evaluated. The computational logic approach is statistically well supported and can be used with the proteomes of other plant species.

Reconciling biodiversity conservation, food production and farmers' demand in agricultural landscapes.

Efficient management of agricultural management should consider multiple services and stakeholders. Yet, it remains unclear how to guarantee ecosystem services for multiple stakeholders' demands, especially considering the observed biodiversity decline following reductions in semi-natural habitat (SNH), and global change. Here, we use an ecosystem service model of intensively-managed agricultural landscapes to derive the best landscape compositions for different stakeholders' demands, and how they vary with stochasticity and the degree of pollination dependence of crops. We analyse three groups of stakeholders assumed to value different ecosystem services most - individual farmers (crop yield per area), agricultural unions (landscape production) and conservationists (biodiversity). Additionally, we consider a social average scenario that aims at maximizing multifunctionality. Trade-offs among stakeholders' demands strongly depend on the degree of pollination dependence of crops, the strength of environmental and demographic stochasticity, and the relative amount of an ecosystem service demanded by each stakeholder. Intermediate amounts of SNH deliver relatively high levels of the three services (social average). Our analysis further suggests that the current levels of SNH protection lie below these intermediate amounts of SNH in intensively-managed agricultural landscapes. Given the worldwide trends in agriculture and global change, current policies should start to consider factors such as crop type and stochasticity, as they can strongly influence best landscape compositions for different stakeholders. Our results suggest ways of managing landscapes to reconcile several actors' demands and ensure for biodiversity conservation and food production.

Reshaping our understanding of species' roles in landscape-scale networks.

In network ecology, landscape-scale processes are often overlooked, yet there is increasing evidence that species and interactions spill over between habitats, calling for further study of interhabitat dependencies. Here, we investigate how species connect a mosaic of habitats based on the spatial variation of their mutualistic and antagonistic interactions using two multilayer networks, combining pollination, herbivory and parasitism in the UK and New Zealand. Developing novel methods of network analysis for landscape-scale ecological networks, we discovered that few plant and pollinator species acted as connectors or hubs, both within and among habitats, whereas herbivores and parasitoids typically have more peripheral network roles. Insect species' roles depend on factors other than just the abundance of taxa in the lower trophic level, exemplified by larger Hymenoptera connecting networks of different habitats and insects relying on different resources across different habitats. Our findings provide a broader perspective for landscape-scale management and ecological community conservation.

Trade-offs in the provisioning and stability of ecosystem services in agroecosystems.

Changes in land use generate trade-offs in the delivery of ecosystem services in agricultural landscapes. However, we know little about how the stability of ecosystem services responds to landscape composition, and what ecological mechanisms underlie these trade-offs. Here, we develop a model to investigate the dynamics of three ecosystem services in intensively managed agroecosystems, i.e., pollination-independent crop yield, crop pollination, and biodiversity. Our model reveals trade-offs and synergies imposed by landscape composition that affect not only the magnitude but also the stability of ecosystem service delivery. Trade-offs involving crop pollination are strongly affected by the degree to which crops depend on pollination and by their relative requirement for pollinator densities. We show conditions for crop production to increase with biodiversity and decreasing crop area, reconciling farmers' profitability and biodiversity conservation. Our results further suggest that, for pollination-dependent crops, management strategies that focus on maximizing yield will often overlook its stability. Given that agriculture has become more pollination-dependent over time, it is essential to understand the mechanisms driving these trade-offs to ensure food security.

Restoration and repair of Earth's damaged ecosystems.

Given that few ecosystems on the Earth have been unaffected by humans, restoring them holds great promise for stemming the biodiversity crisis and ensuring ecosystem services are provided to humanity. Nonetheless, few studies have documented the recovery of ecosystems globally or the rates at which ecosystems recover. Even fewer have addressed the added benefit of actively restoring ecosystems versus allowing them to recover without human intervention following the cessation of a disturbance. Our meta-analysis of 400 studies worldwide that document recovery from large-scale disturbances, such as oil spills, agriculture and logging, suggests that though ecosystems are progressing towards recovery following disturbances, they rarely recover completely. This result reinforces conservation of intact ecosystems as a key strategy for protecting biodiversity. Recovery rates slowed down with time since the disturbance ended, suggesting that the final stages of recovery are the most challenging to achieve. Active restoration did not result in faster or more complete recovery than simply ending the disturbances ecosystems face. Our results on the added benefit of restoration must be interpreted cautiously, because few studies directly compared different restoration actions in the same location after the same disturbance. The lack of consistent value added of active restoration following disturbance suggests that passive recovery should be considered as a first option; if recovery is slow, then active restoration actions should be better tailored to overcome specific obstacles to recovery and achieve restoration goals. We call for a more strategic investment of limited restoration resources into innovative collaborative efforts between scientists, local communities and practitioners to develop restoration techniques that are ecologically, economically and socially viable.

HIV among Black men who have sex with men (MSM) in the United States: a review of the literature.

In 2006, Millett published a seminal literature review that examined 12 hypotheses to explain the high rates of HIV among black MSM. This paper augments Millett's article by reviewing the recent literature on behavioral, biomedical, structural, social contextual, psychosocial, and social network factors that affect HIV rates among black MSM. We searched three databases: PubMed, Scopus, and Google Scholar. First we searched all articles that included black or African American and MSM and HIV. We then searched the following terms for each area: behavioral (drug use during sex, crack cocaine use, and serosorting); biomedical (circumcision, STDs, and STIs); structural (access to care, HIV care, ART, HAART, patient-provider communication, HIV quality of care); social contextual (stigma, discrimination, internalized homophobia, internalized heterosexism, medical mistrust, social isolation, and incarceration); psychosocial (peer support and mental health); and social network (sexual mixing, partner characteristics, and social networks) factors. We identified 39 articles to include in this review. We found inconclusive evidence that incarceration, stigma, discrimination, social isolation, mental health disparities, or social networks explain the elevated rates of HIV among black MSM. We found evidence that the differences in rates of HIV between black and white MSM may be explained by differences in STIs, undiagnosed seropositivity, access to care and treatment services, and use of HAART. There is an overwhelming need for HIV testing, linkage to care, retention in care, and adherence programs for black MSM.

Unmet HIV service needs among Black men who have sex with men in the United States.

The National HIV/AIDS Strategy (NHAS) clearly emphasized the need to provide services to black men who have sex with men (MSM). However, there are no estimates of the unmet HIV-related service delivery needs among black MSM. We estimate that of 195,313 black MSM living with HIV in the US, 50,196 were not yet diagnosed, and 145,118 were aware of their seropositivity (of whom 67,625 were not linked to care and 77,493 were linked to care). Also, of those already diagnosed, ~43,390 had undetectable viral load and 101,728 had detectable viral load. Approximately 19,545 of diagnosed black MSM engage in unprotected risk behavior in serostatus-discordant partnerships. The cost of delivering services needed to meet the NHAS goals is ~$2.475 billion in 2011 U.S. dollars. Mathematical modeling suggests that provisions of these services would avert 6213 HIV infections at an economically favorable cost of $20,032 per quality-adjusted life year saved.

Stability in plant-pollinator communities across organizational levels: present, gaps, and future.

Abstract. The study of ecological stability continues to fill the pages of scientific journals almost seven decades after the first ecologists initiated this line of research. The many advances in this field have focused on understanding the stability of populations, communities or functions within single guilds or trophic levels, with less research conducted across multiple trophic levels and considering the different interactions that relate species to each other. Here, we review the recent literature on the multiple dimensions of ecological stability specifically within plant-pollinator communities. We then focus on one of stability´s dimensions, temporal invariability, and adapt an existing partitioning framework that bridges invariability and synchrony measures across spatial scales and organizational levels to accommodate interactions between plants and their pollinators. Finally, we use this framework to analyse temporal invariability in plant reproductive success, partitioning it on invariability and synchrony components across plant and pollinator populations and communities, as well as their interactions, using a well-resolved dataset that encompasses data for two years. Our review of the literature points to several significant gaps in our current knowledge, with simulation studies clearly overrepresented in the literature as opposed to experimental or empirical approaches. Our quantitative approach to partitioning invariability shows similar patterns of decreasing temporal invariability across increasing organizational levels driven by asynchronous dynamics amongst populations and communities, which overall stabilize ecosystem functioning (plant reproductive success). This study represents a first step towards a better comprehension of temporal invariability in ecosystem functions defined by interactions between species and provides a blueprint for the type of spatially replicated multi-year data that needs to be collected in the future to further our understanding of ecological stability within multi-trophic communities.

A systematic review of HIV interventions for black men who have sex with men (MSM).

BACKGROUND: Black men who have sex with men (MSM) are disproportionately burdened by HIV/AIDS. Despite this burden there has been a shortage of research on HIV interventions for black MSM. This article provides a comprehensive review of the literature on interventions for black MSM to identify effective HIV prevention intervention strategies for black MSM. METHODS: We searched 3 databases: Pubmed, Scopus, and Google Scholar to identify peer-reviewed articles and used the following search terms: African American or black; MSM or men who have sex with men and women (MSMW); HIV; program or intervention; and evaluation or intervention science or implementation research. We included research articles that assessed interventions for black men who have sex with men. We included studies that used an experimental, quasi-experimental, or pre-post test design as well as formative research studies. We also searched the CDC and NIH websites to identify planned and on-going intervention studies. We identified a total of 23 studies to include in the review. RESULTS: We identified 12 completed studies of interventions for black MSM. Eight of these 12 interventions aimed to reduce HIV risk behaviors and 5 found a significant reduction in HIV risk behavior over time. We identified 4 health service intervention studies for young black MSM. CONCLUSIONS: Behavior change interventions are effective at reducing HIV risk behaviors among black MSM. However, relying only on behavioral interventions that aim to reduce HIV risk behavior will most likely not have a population-level effect on HIV infection among black MSM. There is a compelling and urgent need to develop and test comprehensive HIV testing, linkage to care, retention in care and adherence interventions for black MSM.

MILimbEEG: A dataset of EEG signals related to upper and lower limb execution of motor and motor imagery tasks.

Biomedical Electroencephalography (EEG) signals are the result of measuring the electric potential difference generated on the scalp surface by neural activity corresponding to each brain area. Accurate and automatic detection of neural activity from the upper and lower limbs using EEG may be helpful in rehabilitating people suffering from mobility limitations or disabilities. This article presents a dataset containing 7440 CSV files from 60 test subjects during motor and motor imagery tasks. The motor and motor imagery tasks performed by the test subjects were: Closing Left Hand (CLH), Closing Right Hand (CRH), Dorsal flexion of Left Foot (DLF), Plantar flexion of Left Foot (PLF), Dorsal flexion of Right Foot (DRF), Plantar flexion of Right Foot (PRF) and Resting in between tasks (Rest). The volunteers were recruited from research colleagues at ESPOL and patients at the Luis Vernaza Hospital in Guayaquil, Ecuador. Each CSV file has 501 rows, of which the first one lists the electrodes from 0 to 15, and the remaining 500 rows correspond to 500 data recorded during the task is performed due to sample rate. In addition, each file has 17 columns, of which the first one indicates the sampling number and the remaining 16 columns represent 16 surface EEG electrodes. As a data recording equipment, the OpenBCI is used in a monopolar setup with a sampling rate of 125 Hz. This work includes statistical measures about the demographic information of all recruited test subjects. Finally, we outline the experimental methodology used to record EEG signals during upper and lower limb task execution. This dataset is called MILimbEEG and contains microvolt (µV) EEG signals acquired during motor and motor imagery tasks. The collected data may facilitate the evaluation of EEG signal detection and classification models dedicated to task recognition.

The role of the anterior cingulate cortex in emotional response inhibition.

Although the involvement of the anterior cingulate cortex (ACC) in emotional response inhibition is well established, there are several outstanding issues about the nature of this involvement that are not well understood. The present study aimed to examine the precise contribution of the ACC to emotion-modulated response inhibition by capitalizing on fine temporal resolution of the event-related potentials (ERPs) and the recent advances in source localization. To this end, participants (N = 30) performed an indirect affective Go/Nogo task (i.e., unrelated to the emotional content of stimulation) that required the inhibition of a motor response to three types of visual stimuli: arousing negative (A-), neutral (N), and arousing positive (A+). Behavioral data revealed that participants made more commission errors to A+ than to N and A-. Electrophysiological data showed that a specific region of the ACC at the intersection of its dorsal and rostral subdivisions was significantly involved in the interaction between emotional processing and motor inhibition. Specifically, activity reflecting this interaction was observed in the P3 (but not in the N2) time range, and was greater during the inhibition of responses to A+ than to N and A-. Additionally, regression analyses showed that inhibition-related activity within this ACC region was associated with the emotional content of the stimuli (its activity increased as stimulus valence was more positive), and also with behavioral performance (both with reaction times and commission errors). The present results provide additional data for understanding how, when, and where emotion interacts with response inhibition within the ACC.

Genome-Wide Association Study of Listeria monocytogenes Isolates Causing Three Different Clinical Outcomes.

Heterogeneity in virulence potential of L. monocytogenes subgroups have been associated with genetic elements that could provide advantages in certain environments to invade, multiply, and survive within a host. The presence of gene mutations has been found to be related to attenuated phenotypes, while the presence of groups of genes, such as pathogenicity islands (PI), has been associated with hypervirulent or stress-resistant clones. We evaluated 232 whole genome sequences from invasive listeriosis cases in human and ruminants from the US and Europe to identify genomic elements associated with strains causing three clinical outcomes: central nervous system (CNS) infections, maternal-neonatal (MN) infections, and systemic infections (SI). Phylogenetic relationships and virulence-associated genes were evaluated, and a gene-based and single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) were conducted in order to identify loci associated with the different clinical outcomes. The orthologous results indicated that genes of phage phiX174, transfer RNAs, and type I restriction-modification (RM) system genes along with SNPs in loci involved in environmental adaptation such as rpoB and a phosphotransferase system (PTS) were associated with one or more clinical outcomes. Detection of phenotype-specific candidate loci represents an approach that could narrow the group of genetic elements to be evaluated in future studies.