Genetic and environmental influences on premature death in adult adoptees

Biomarker Panels in Critical Care

Biomarker panels have the potential to advance the field of critical care medicine by stratifying patients according to prognosis and/or underlying pathophysiology. This article discusses the discovery and validation of biomarker panels, along with their translation to the clinical setting. The current literature on the use of biomarker panels in sepsis, acute respiratory distress syndrome, and acute kidney injury is reviewed.

Sepsis and septic shock: current approaches to management

Sepsis, defined as life-threatening organ dysfunction due to a dysregulated host response to infection, is recognised by the World Health Organization as a global health priority. Each year, 5000 of the 18 000 adults with sepsis treated in Australian intensive care units die, with survivors suffering long-term physical, cognitive and psychological dysfunction, which is poorly recognised and frequently untreated. There are currently no effective pharmacological treatments for sepsis, making early recognition, resuscitation and immediate treatment with appropriate antibiotics the key to reducing the burden of resulting disease. The majority of sepsis, around 70-80%, is community acquired making emergency departments and primary care key targets to improve recognition and early management. Case fatality rates for sepsis are decreasing in many countries with the reduction attributed to national or regional screening and quality improvement programmes focused on early identification and immediate treatment. The optimum approach to treating established sepsis has been informed by high-quality, multicentre investigator initiated randomised trials with much of the valuable data coming from National Health and Medical Research Council-funded trials run from Australia. While early recognition and improved management of the acute episode are important steps in reducing death and disability from sepsis, a substantial reduction in the burden of sepsis-related disease requires action across the entire healthcare system. In this narrative review, we provide a summary of current knowledge on epidemiology of sepsis and septic shock and recommendations on the optimum approach to the management of these conditions in adults.

Transcriptome Meta-Analysis Deciphers a Dysregulation in Immune Response-Associated Gene Signatures during Sepsis

Sepsis is a life-threatening disease induced by a systemic inflammatory response, which leads to organ dysfunction and mortality. In sepsis, the host immune response is depressed and unable to cope with infection; no drug is currently available to treat this. The lungs are frequently the starting point for sepsis. This study aimed to identify potential genes for diagnostics and therapeutic purposes in sepsis by a comprehensive bioinformatics analysis. Our criteria are to unravel sepsis-associated signature genes from gene expression datasets. Differentially expressed genes (DEGs) were identified from samples of sepsis patients using a meta-analysis and then further subjected to functional enrichment and protein‒protein interaction (PPI) network analysis for examining their potential functions. Finally, the expression of the topmost upregulated genes (ARG1, IL1R2, ELANE, MMP9) was quantified by reverse transcriptase-PCR (RT-PCR), and myeloperoxidase (MPO) expression was confirmed by immunohistochemistry (IHC) staining in the lungs of a well-established sepsis mouse model. We found that all the four genes were upregulated in semiquantitative RT-PCR studies; however, MMP9 showed a nonsignificant increase in expression. MPO staining showed strong immunoreactivity in sepsis as compared to the control. This study demonstrates the role of significant and widespread immune activation (IL1R2, MMP9), along with oxidative stress (ARG1) and the recruitment of neutrophils, in sepsis (ELANE, MPO).

A large-scale genomic investigation of susceptibility to infection and its association with mental disorders in the Danish population

Infections and mental disorders are two of the major global disease burdens. While correlations between mental disorders and infections have been reported, the possible genetic links between them have not been assessed in large-scale studies. Moreover, the genetic basis of susceptibility to infection is largely unknown, as large-scale genome-wide association studies of susceptibility to infection have been lacking. We utilized a large Danish population-based sample (N = 65,534) linked to nationwide population-based registers to investigate the genetic architecture of susceptibility to infection (heritability estimation, polygenic risk analysis, and a genome-wide association study (GWAS)) and examined its association with mental disorders (comorbidity analysis and genetic correlation). We found strong links between having at least one psychiatric diagnosis and the occurrence of infection (P = 2.16 × 10-208, OR = 1.72). The SNP heritability of susceptibility to infection ranged from ~2 to ~7% in samples of differing psychiatric diagnosis statuses (suggesting the environment as a major contributor to susceptibility), and polygenic risk scores moderately but significantly explained infection status in an independent sample. We observed a genetic correlation of 0.496 (P = 2.17 × 10-17) between a diagnosis of infection and a psychiatric diagnosis. While our GWAS did not identify genome-wide significant associations, we found 90 suggestive (P ≤ 10-5) associations for susceptibility to infection. Our findings suggest a genetic component in susceptibility to infection and indicate that the occurrence of infections in individuals with mental illness may be in part genetically driven.

Precision Medicine in Critical Illness: Sepsis and Acute Respiratory Distress Syndrome

Sepsis and the acute respiratory distress syndrome (ARDS) each cause substantial morbidity and mortality. In contrast to other lung diseases, the entire course of disease in these syndromes is measured in days to weeks rather than months to years, which raises unique challenges in achieving precision medicine. We review advances in sepsis and ARDS resulting from omics studies, including those involving genome-wide association, gene expression, targeted proteomics, and metabolomics approaches. We focus on promising evidence of biological subtypes in both sepsis and ARDS that consistently display high risk for death. In sepsis, a gene expression signature with dysregulated adaptive immune signaling has evidence for a differential response to systemic steroid therapy, whereas in ARDS, a hyperinflammatory pattern identified in plasma using targeted proteomics responded more favorably to randomized interventions including high positive end-expiratory pressure, volume conservative fluid therapy, and simvastatin therapy. These early examples suggest heterogeneous biology that may be challenging to detect by clinical factors alone and speak to the promise of a precision approach that targets the right treatment at the right time to the right patient.

Host susceptibility to severe influenza A virus infection

Most people exposed to a new flu virus do not notice any symptoms. A small minority develops critical illness. Some of this extremely broad variation in susceptibility is explained by the size of the initial inoculum or the influenza exposure history of the individual; some is explained by generic host factors, such as frailty, that decrease resilience following any systemic insult. Some demographic factors (pregnancy, obesity, and advanced age) appear to confer a more specific susceptibility to severe illness following infection with influenza viruses. As with other infectious diseases, a substantial component of susceptibility is determined by host genetics. Several genetic susceptibility variants have now been reported with varying levels of evidence. Susceptible hosts may have impaired intracellular controls of viral replication (e.g. IFITM3, TMPRS22 variants), defective interferon responses (e.g. GLDC, IRF7/9 variants), or defects in cell-mediated immunity with increased baseline levels of systemic inflammation (obesity, pregnancy, advanced age). These mechanisms may explain the prolonged viral replication reported in critically ill patients with influenza: patients with life-threatening disease are, by definition, abnormal hosts. Understanding these molecular mechanisms of susceptibility may in the future enable the design of host-directed therapies to promote resilience.

Genomic medicine in Chagas disease

Genetic approaches have been proposed for improving the understanding of the causes of differential susceptibility to Trypanosoma cruzi infection and Chagas disease outcome. Polymorphisms in genes involved in the immune/inflammatory response are being studied in order to clarify their possible role in the occurrence or severity of the cardiac and/or gastrointestinal complications. However still today, the number of significant associated genes is limited and the pathophysiological mechanisms underlying this condition are unknown. This article review the information currently available from the published scientific literature regarding the genetic variants of molecules of the immune system and other variants that can contribute to the clinical presentation of the disease. Genomic medicine will improve our knowledge about the molecular basis of Chagas disease, will open new avenues for developing biomarkers of disease progression, new therapeutic strategies to suit the requirements of individual patients, and will contribute to the control of one of the infections with the greatest socio-economic impact in the Americas.

The Importance of Sex Differences on Outcome after Major Trauma: Clinical Outcome in Women Versus Men

Purpose: The purpose of this study was to evaluate epidemiological and clinically relevant sex-related differences in polytraumatized patients at a Level 1 Trauma Center. Methods: 646 adult patients (210 females and 436 males) who were classified as polytraumatized (at the point of admission) and treated at our Level I Trauma Center were reviewed and included in this study. Demographic data as well as mechanism of injury, injury severity, injury pattern, frequency of preclinical intubation, hemodynamic variables on admission, time of mechanical ventilation and of intensive care unit (ICU) treatment, as well as the incidence of acute respiratory distress syndrome (ARDS), multi organ failure (MOF), and mortality were extracted and analyzed. Results: A total of 210 female and 436 male patients formed the basis of this report. Females showed a higher mean age (44.6 vs. 38.3 years; p < 0.0001) than their male counterparts. Women were more likely to be injured as passengers or by suicidal falls whereas men were more likely to suffer trauma as motorcyclists. Following ICU treatment, female patients resided significantly longer at the casualty ward than men (27.1 days vs. 20.4 days, p = 0.013) although there was no significant difference regarding injury severity, hemodynamic variables on admission, and incidence of MOF, ARDS, and mortality. Conclusion: The positive correlation of higher age and longer in-hospital stay in female trauma victims seems to show women at risk for a prolonged in-hospital rehabilitation time. A better understanding of the impact of major trauma in women (but also men) will be an important component of efforts to improve trauma care and long-term outcome.

Toll-like receptor polymorphism in host immune response to infectious diseases: A review

Immunopolymorphism is considered as an important aspect behind the resistance or susceptibility of the host to an infectious disease. Over the years, researchers have explored many genetic factors for their role in immune surveillance against infectious diseases. Polymorphic characters in the gene encoding Toll-like receptors (TLRs) play profound roles in inducing differential immune responses by the host against parasitic infections. Protein(s) encoded by TLR gene(s) are immensely important due to their ability of recognizing different types of pathogen associated molecular patterns (PAMPs). This study reviews the polymorphic residues present in the nucleotide or in the amino acid sequence of TLRs and their influence on alteration of inflammatory signalling pathways promoting either susceptibility or resistance to major infectious diseases, including tuberculosis, leishmaniasis, malaria and filariasis. Population-based studies exploring TLR polymorphisms in humans are primarily emphasized to discuss the association of the polymorphic residues with the occurrence and epidemiology of the mentioned infectious diseases. Principal polymorphic residues in TLRs influencing immunity to infection are mostly single nucleotide polymorphisms (SNPs). I602S (TLR1), R677W (TLR2), P554S (TLR3), D299G (TLR4), F616L (TLR5), S249P (TLR6), Q11L (TLR7), M1V (TLR8), G1174A (TLR9) and G1031T (TLR10) are presented as the major influential SNPs in shaping immunity to pathogenic infections. The contribution of these SNPs in the structure-function relationship of TLRs is yet not clear. Therefore, molecular studies on such polymorphisms can improve our understanding on the genetic basis of the immune response and pave the way for therapeutic intervention in a more feasible way.

Host genetic variants in sepsis risk: a field synopsis and meta-analysis

Background

Published data revealed that host genetic variants have a substantial influence on sepsis susceptibility. However, the results have been inconsistent. We aimed to systematically review the published studies and quantitatively evaluate the effects of these variants on the risk of sepsis.

Methods

We searched the PubMed, EMBASE, Medline, Web of Knowledge, and HuGE databases to identify studies that investigated the associations between genetic variants and sepsis risk. Then, we conducted meta-analyses of the associations for genetic variants with at least three study populations and applied the Venice criteria to assess the association result credibility.

Results

A literature search identified 349 eligible articles that investigated 405 variants of 172 distinct genes. We performed 204 primary and 185 subgroup meta-analyses for 76 variants of 44 genes. The results showed that 29 variants of 23 genes were significantly associated with the risk of sepsis, including 8 variants of pattern recognition receptors (PRRs), 14 variants of cytokines, one variant of an immune-related gene and 6 variants of other genes. Furthermore, the cumulative epidemiological evidence of a significant association between each variant and the risk of sepsis was classified as strong or moderate for 18 variants. For the 329 variants with fewer than three study populations, 63 variants of 48 genes have been reported to be significantly associated with the risk of sepsis in a systematic review.

Conclusion

We identified several genetic variants that could influence the susceptibility to sepsis by systematic review and meta-analysis. This study provides a comprehensive overview of the genetic architecture of variants involved in sepsis susceptibility and novel insight that may affect personalized targeted treatment in the future clinical management of sepsis.

Electronic supplementary material

The online version of this article (10.1186/s13054-019-2313-0) contains supplementary material, which is available to authorized users.

A Sex-Stratified Genome-Wide Association Study of Tuberculosis Using a Multi-Ethnic Genotyping Array

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as high in males than in females. While socio-economic status, behavior and sex hormones influence the male bias they do not fully account for it. Males have only one copy of the X chromosome, while diploid females are subject to X chromosome inactivation. In addition, the X chromosome codes for many immune-related genes, supporting the hypothesis that X-linked genes could contribute to TB susceptibility in a sex-biased manner. We report the first TB susceptibility genome-wide association study (GWAS) with a specific focus on sex-stratified autosomal analysis and the X chromosome. A total of 810 individuals (410 cases and 405 controls) from an admixed South African population were genotyped using the Illumina Multi Ethnic Genotyping Array, specifically designed as a suitable platform for diverse and admixed populations. Association testing was done on the autosome (8,27,386 variants) and X chromosome (20,939 variants) in a sex stratified and combined manner. SNP association testing was not statistically significant using a stringent cut-off for significance but revealed likely candidate genes that warrant further investigation. A genome wide interaction analysis detected 16 significant interactions. Finally, the results highlight the importance of sex-stratified analysis as strong sex-specific effects were identified on both the autosome and X chromosome.

Epidemiology of community-acquired sepsis in the Faroe Islands - a prospective observational study

INTRODUCTION

The aim of the study was to gather nation-wide epidemiological and clinical data in order to characterize community-acquired sepsis in the Faroe Islands, and to compare these data with epidemiological studies performed in other geographical areas.

METHODS

A prospective, observational study conducted from October 2013 until April 2015 to characterize sepsis, and to calculate incidence rates for community-acquired sepsis of any severity, community-acquired severe sepsis, community-acquired septic shock and community-acquired sepsis without community-acquired severe sepsis or community-acquired septic shock.

RESULTS

Of 5279 admissions, 583 cases fulfilled the criteria for community-acquired sepsis of any severity. The mean age of all cases was 67.6 ± 18.3 years. Men accounted for 298 (51.5%) admissions. Charlson comorbidity index was greater than 2 in 247 (42.4%) cases. The incidence of community-acquired sepsis of any severity was 1414/100,000 person-years at risk (95% CI, 1374-1440). The incidence rate for community-acquired sepsis without community-acquired severe sepsis and community-acquired septic shock was 719/100,000 person-years at risk (95% CI, 695-742), for community-acquired severe sepsis 644/100,000 person-years at risk (95% CI, 623-668), for community-acquired septic shock 51/100,000 person-years at risk (95% CI, 45-58). The highest incidence was seen in elderly patients.

CONCLUSION

The incidence rates were slightly higher in men and increased with age, especially in those older than 85 years. Incidence rates of sepsis of any severity were higher than previously published from other countries.

Association between the T6459C point mutation of the mitochondrial MT-CO1 gene and susceptibility to sepsis among Chinese Han people

To search for an association between sepsis and mitochondrial genetic basis, we began our study. In this study, a proband harbouring mitochondrial T6459C mutation with sepsis and his Chinese Han pedigree including 7 members of 3 generations were enrolled. General information, blood parameters and mitochondrial full sequence scanning of all members were performed, and cellular functions, including cellular reactive oxygen species (ROS) levels, mitochondrial membrane potential (MMP), degrees of cell apoptosis and adenosine triphosphate (ATP) concentrations, were measured in members with and without the T6459C mutation. Through mitochondrial full sequence scanning and analysis of all members we found, the maternal members (I-1, II-1, II-2 and II-4) in this Chinese Han pedigree all had the mitochondrial T6459C mutation and were used as the mutation group. The non-maternal members (II-3, III-1 and III-2) did not have this mutation and were used as the non-mutation group. The differences in all indicators, including the blood routine, blood biochemistry and coagulation function tests, between members in these two groups were not significant. Under the non-stimulation condition, the mutation group had higher ROS levels (4210.42 ± 1043.35 vs 3387.78 ± 489.66, P = .028) and apoptosis ratios (P = .004) and lower ATP concentrations (P = .049) and MMP levels (P = .047) than the non-mutation group. After 6 hours of simulated LPS stimulation, the mutation group had significantly increased ROS levels (5759.25 ± 2297.90 vs 3862.00 ± 1519.77, P = .045) compared with the non-mutation group, whereas the mutation group continued to demonstrate higher ROS levels (P = .045) and apoptosis ratios (P = .003) and lower MMP levels (P = .005) and ATP concentrations (P = .010). We speculated that the mtDNA T6459C mutation might be the basis for the genetic susceptibility to sepsis.

Cardiovascular Disease Among Women Who Gave Birth to an Infant With a Major Congenital Anomaly

Importance

Having a child with a major birth defect can be a life-changing and stressful event that may be associated with higher cardiovascular disease (CVD) risk, yet the long-term burden of CVD for the child's mother is unknown.

Objective

To assess whether mothers of an infant born with a major congenital anomaly are at higher risk of CVD compared with a comparison cohort.

Design, Setting, and Participants

A population-based cohort study using individual-level linked registry data in Denmark included 42 943 women who gave birth to an infant with a major congenital anomaly between January 1, 1979, and December 31, 2013; and follow-up was conducted until 2015. A comparison group, comprising 428 401 randomly selected women, was 10:1 matched to each affected mother by maternal age, parity, and her infant's year of birth. Data analyses were performed between November 1, 2017, and February 28, 2018.

Exposures

Live birth of an infant with a major congenital anomaly.

Main Outcomes and Measures

The primary outcome was a CVD composite outcome of acute myocardial infarction, coronary revascularization, or stroke. Secondary outcomes included individual components of the CVD composite and other cardiovascular outcomes, including unstable angina, congestive heart failure, atrial fibrillation, peripheral artery disease, ischemic heart disease, and aortic aneurysm. Cox proportional hazards regression analyses generated hazard ratios (HRs), adjusted for maternal demographic, socioeconomic, and chronic health indicators.

Results

Median maternal age at baseline was 28.8 years (interquartile range, 25.3-32.5 years). After a median follow-up of 19.5 years (interquartile range, 9.9-27.6 years), 914 women whose infant had a major congenital anomaly experienced a CVD event (1.21 per 1000 person-years; 95% CI, 1.13-1.28 per 1000 person-years) vs 7516 women in the comparison group (0.99 per 1000 person-years; 95% CI, 0.97-1.01 per 1000 person-years), corresponding to an unadjusted HR of 1.23 (95% CI, 1.15-1.32), and an adjusted HR (aHR) of 1.15 (95% CI, 1.07-1.23). Women who gave birth to an infant with multiorgan anomalies had an even higher aHR (1.37; 95% CI, 1.08-1.72). Mothers of infants with a major anomaly also had an increased aHR of the individual components of the composite outcome and the other cardiovascular outcomes.

Conclusions and Relevance

Women whose child had a major congenital anomaly experienced a 15% to 37% higher risk of premature cardiovascular disease. These women may benefit from targeted interventions aimed at improving their cardiovascular health.

Genetic Predisposition to Infectious Disease

In contemporary medical practice, approaches to infectious disease management have been primarily rooted in a pathogen-centered model. However, host genetics also contribute significantly to infectious disease burden. The fast expansion of bioinformatics techniques and the popularization of the genome-wide association study (GWAS) in recent decades have allowed for rapid and affordable high-throughput genomic analyses. This review focuses on the host model of infectious disease with particular emphasis placed on the genetic variations underlying observed infectious disease predisposition. First, we introduce observational twin-twin concordance studies of diseases such as poliomyelitis, tuberculosis, and hepatitis which suggest the important role of host genetics. We review the well-established links between specific genetic alterations and predisposition to malaria (P. falciparum and P. vivax), Creutzfeldt-Jacob disease (CJD), human immunodeficiency virus (HIV), and Norwalk virus. Finally, we discuss the novel findings yielded by modern GWAS studies, which suggest the strong contribution of immunologic variation in the major histocompatibility complex (MHC) to host genetic infectious disease susceptibility. Future large-scale genomic studies hold promise in providing insights into immunology-pathogen links and may allow for the development of personalized genomic approaches to infectious disease prevention and treatment.

Genetic Susceptibility to Leprosy-From Classic Immune-Related Candidate Genes to Hypothesis-Free, Whole Genome Approaches

Genetics plays a crucial role in controlling susceptibility to infectious diseases by modulating the interplay between humans and pathogens. This is particularly evident in leprosy, since the etiological agent, Mycobacterium leprae, displays semiclonal characteristics not compatible with the wide spectrum of disease phenotypes. Over the past decades, genetic studies have unraveled several gene variants as risk factors for leprosy per se, disease clinical forms and the occurrence of leprosy reactions. As expected, several of these genes are immune-related; yet, hypothesis-free approaches have led to genes not classically linked to immune response. The PARK2, originally described as a Parkinson's disease gene, illustrates the case: Parkin-the protein coded by PARK2-was defined as an important player regulating innate and adaptive immune responses only years after its description as a leprosy susceptibility gene. Interestingly, even with the use of powerful hypothesis-free study designs such as genome-wide association studies, most of the major gene effect controlling leprosy susceptibility remains elusive. One hypothesis to explain this "hidden heritability" is that rare variants not captured by classic association studies are of critical importance. To address this question, massively parallel sequencing of large segments of the human genome-even whole exomes/genomes-is an alternative to properly identify rare, disease-causing mutations. These mutations may then be investigated through sophisticated approaches such as cell reprogramming and genome editing applied to create in vitro models for functional leprosy studies.

Centenarians Overexpress Pluripotency-Related Genes

Human mesenchymal cells can become pluripotent by the addition of Yamanaka factors OCT3/4, SOX2, c-MYC, KLF4. We have recently reported that centenarians overexpress BCL-xL, which has been shown to improve pluripotency; thus, we aimed to determine the expression of pluripotency-related genes in centenarians. We recruited 22 young, 32 octogenarian, and 47 centenarian individuals and determined the mRNA expression of Yamanaka factors and other stemness-related cell surface marker genes (VIM, BMP4, NCAM, BMPR2) in peripheral blood mononuclear cells by reverse transcription polymerase chain reaction. We found that centenarians overexpress OCT3/4, SOX2, c-MYC, VIM, BMP4, NCAM, and BMPR2, when compared with octogenarians (p < .05). We further tested the functional role of BCL-xL in centenarians’ ability to express pluripotency-related genes: lymphocytes from octogenarians transduced with BCL-xL overexpressed SOX2, c-MYC, and KLF4. We conclude that centenarians overexpress Yamanaka Factors and other stemness-related cell surface marker genes, which may contribute to their successful aging.

Early Diagnosis of Sepsis: Is an Integrated Omics Approach the Way Forward?

Sepsis remains one of the leading causes of death in the USA and it is expected to get worse as the population ages. Moreover, the standard of care, which recommends aggressive treatment with appropriate antibiotics, has led to an increase in multiple drug-resistant organisms. There is a dire need for the development of new antibiotics, improved antibiotic stewardship, and therapies that treat the host response. Development of new sepsis therapeutics has been a disappointment as no drugs are currently approved to treat the various complications from sepsis. Much of the failure has been blamed on animal models that do not accurately reflect the course of the disease. However, recent improvements in metabolomic, transcriptomic, genomic, and proteomic platforms have allowed for a broad-spectrum look at molecular changes in the host response using clinical samples. Integration of these multi-omic datasets allows researchers to perform systems biology approaches to identify novel pathophysiology of the disease. In this review, we highlight what is currently known about sepsis and how integrative omics has identified new diagnostic and predictive models of sepsis as well as novel mechanisms. These changes may improve patient care as well as guide future preclinical analysis of sepsis.

Adults with septic shock and extreme hyperferritinemia exhibit pathogenic immune variation

Post-hoc subgroup analysis of the negative trial of interleukin-1β receptor antagonist (IL1RA) for septic shock suggested that patients with features of macrophage activation syndrome (MAS) experienced a 50% relative risk reduction for mortality with treatment. Here we seek a genetic basis for this differential response. From 1341 patients enrolled in the ProCESS trial of early goal directed therapy for septic shock, we selected 6 patients with MAS features and the highest ferritin, for whole exome sequencing (mean 24,030.7 ηg/ml, +/SEM 7,411.1). Eleven rare (minor allele frequency <5%) pathogenic or likely pathogenic variants causal for the monogenic disorders of Familial Hemophagocytic Lymphohistiocytosis, atypical Hemolytic Uremic Syndrome, Familial Mediterranean Fever, and Cryopyrin-associated Periodic Fever were identified. In these conditions, seven of the identified variants are currently targeted with IL1RA and four with anti-C5 antibody. Gene-targeted precision medicine may benefit this subgroup of patients with septic shock and pathogenic immune variation.

Sepsis Diagnostics in the Era of "Omics" Technologies

Sepsis is a multifactorial clinical syndrome with an extremely dynamic clinical course and with high diverse clinical phenotype. Early diagnosis is crucial for the final clinical outcome. Previous studies have not identified a biomarker for the diagnosis of sepsis which would have sufficient sensitivity and specificity. Identification of the infectious agents or the use of molecular biology, next gene sequencing, has not brought significant benefit for the patient in terms of early diagnosis. Therefore, we are currently searching for biomarkers, through "omics" technologies with sufficient diagnostic specificity and sensitivity, able to predict the clinical course of the disease and the patient response to therapy. Current progress in the use of systems biology technologies brings us hope that by using big data from clinical trials such biomarkers will be found.

Mortality Among Mothers Whose Children Were Taken Into Care by Child Protection Services: A Discordant Sibling Analysis

This study examines whether mothers who had a child taken into care by child protection services have higher mortality rates compared with rates seen in their biological sisters who did not have a child taken into care. We conducted this retrospective cohort study using linkable administrative data from 3,948 mothers whose oldest child was born in Manitoba, Canada, between April 1, 1992, and March 31, 2015. These mothers were from 1,974 families in which one sister had a child taken into care and one sister did not. We computed rate differences and hazard ratios of all-cause, avoidable, and unavoidable mortality. There were an additional 24 deaths per 10,000 person-years among mothers who had had a child taken into care. Mothers who had a child taken into care had higher rates of mortality due to avoidable causes (hazard ratio = 3.46; 95% confidence interval: 1.41, 8.48) and unavoidable causes (hazard ratio = 2.92; 95% confidence interval: 1.01, 8.44). The number of children taken into care did not affect mortality rates among mothers with at least 1 child taken into care. The higher mortality rates-particularly avoidable mortality-among mothers who had a child taken into care indicate a need for more specific interventions for these mothers.

Genomic prediction of avian influenza infection outcome in layer chickens

Avian influenza (AI) is a devastating poultry disease that currently can be controlled only by liquidation of affected flocks. In spite of typically very high mortality rates, a group of survivors was identified and genotyped on a 600K single nucleotide polymorphism (SNP) chip to identify genetic differences between survivors, and age- and genetics-matched controls from unaffected flocks. In a previous analysis of this dataset, a heritable component was identified and several regions that are associated with outcome of the infection were localized but none with a large effect. For complex traits that are determined by many genes, genomic prediction models using all SNPs across the genome simultaneously are expected to optimally exploit genomic information. In this study, we evaluated the diagnostic value of genomic estimated breeding values for predicting AI infection outcome within and across two highly pathogenic avian influenza viral strains and two genetic lines of layer chickens using receiver operating curves. We show that genomic prediction based on the 600K SNP chip has the potential to predict disease outcome especially within the same strain of virus (area under receiver operating curve above 0.7), but did not predict well across genetic varieties (area under receiver operating curve of 0.43).

Leptin receptor q223r polymorphism influences neutrophil mobilization after Clostridium difficile infection

Clostridium difficile is the leading cause of nosocomial infections in the United States. Clinical disease outcomes after C. difficile infection (CDI) are dependent on intensity of host inflammatory responses. Specifically, peak peripheral white blood cell (WBC) count >20 × 10⁹ l^-1 is an indicator of adverse outcomes in CDI patients, and is associated with higher 30-day mortality. We show that homozygosity for a common single nucleotide polymorphism (Q to R mutation in leptin receptor that is present in up to 50% of people), significantly increases the risk of having peak peripheral WBC count >20 × 10⁹ l^-1 (odds ratio=5.41; P=0.0023) in CDI patients. In a murine model of CDI, we demonstrate that mice homozygous for the same single nucleotide polymorphism (RR mice) have more blood and tissue leukocytes (specifically neutrophils), exaggerated tissue inflammation, and higher mortality as compared with control mice, despite similar pathogen burden. Further, we show that neutrophilia in RR mice is mediated by gut microbiota-directed expression of CXC chemokine receptor 2 (CXCR2), which promotes the release of neutrophils from bone marrow reservoir. Overall these studies provide novel mechanistic insights into the role of human genetic polymorphisms and gut microbiota in regulating the fundamental biological process of CDI-induced neutrophilia.

Delayed age at transfer of adoptees to adoptive parents is associated with increased mortality irrespective of social class of the adoptive parents: a cohort study

BACKGROUND

Adverse early life experience and development may have long-term health consequences, but later environmental conditions may perhaps protect against the effects of such early life adversities. The aim was to investigate whether cause-specific and overall mortality rates among adoptees are associated with the age at which they were transferred to the adoptive family and whether the social class of the adoptive family modifies this association.

METHODS

A cohort of 10,592 non-familial adoptions (biologically unrelated adoptee and adoptive parents) of Danish-born children formally granted in 1924-47 and with follow-up of total and cause-specific mortality through ages up to 85 years. The rates of death after the age of 16 from all causes combined, all natural causes, all external causes, and suicide were compared according to the age at which adoptees were transferred to their adoptive family by estimating hazard ratios in Cox regression models.

RESULTS

Death rates from all causes were significantly higher in adoptees transferred between age 1 month and 4 years compared to those transferred immediately after birth with the hazard ratio peaking at 1.19 (95% confidence limit: 1.08 to 1.32) for adoptees transferred between 6 and 11 months. This result was primarily driven by a similar pattern for natural causes of death. For death from external causes and for suicide the hazard ratios were increasing with increasing age at transfer, and tests for trend were statistically significant. The social class of the adoptive family did not significantly modify these associations.

CONCLUSIONS

Transfer to an adoptive family later than at the time of birth may have adverse long-term consequences affecting overall and cause-specific mortality. These effects were not modified by the environment provided by the adoptive family as indicated by the social class of these families.

Serial Changes in Mannose-Binding Lectin in Patients with Sepsis

Background

Mannose-binding lectin (MBL) deficiency leads to increased susceptibility to infection. We investigated whether serial changes in MBL levels are associated with the prognosis of patients diagnosed with septic shock, and correlated with cytokine levels.

Methods

We enrolled 131 patients with septic shock in the study. We analyzed the serum samples for MBL and cytokine levels at baseline and 7 days later. Samples on day 7 were available in 73 patients.

Results

We divided the patients with septic shock into four groups according to serum MBL levels (<1.3 µg/mL or ≥1.3 µg/mL) on days 1 and 7. Patients with low MBL levels on day 1 and high MBL levels on day 7 showed a favorable prognosis for 28-day survival (odds ratio, 1.96, 95% confidence interval, 1.10–2.87; p=0.087). The high MBL group on day 7 showed a significant decrease in monocyte chemoattractant protein 1, interleukin (IL)-1β, IL-6, IL-8, interferon-γ, and granulocyte macrophage colony-stimulating factor levels compared with the low MBL group on day 7.

Conclusion

The increase in MBL levels of patients with septic shock may suggest a favorable prognosis and attenuate pro-inflammatory and anti-inflammatory responses.

Treatment outcomes of tuberculosis patients under directly observed treatment short-course at Debre Tabor General Hospital, northwest Ethiopia: nine-years retrospective study

BACKGROUND

Data regarding tuberculosis (TB) treatment outcomes, proportion of TB/HIV co-infection and associated factors have been released at different TB treatment facilities in Ethiopia and elsewhere in the world as part of the auditing and surveillance service. However, these data are missing for the TB clinic offering directly observed treatment short-course (DOTs) at Debre Tabor General Hospital (DTGH).

METHODS

The authors analysed the records of 985 TB patients registered at the DTGH from September 2008 to December 2016. Data on patients' sex, age, type of TB, and treatment outcomes were extracted from the TB treatment registration logbook. The treatment outcome of patients was categorized according to the National TB and Leprosy Control Program guidelines: cured, treatment completed, treatment failed, died, and not evaluated (transferred out and unknown cases).

RESULTS

Around half of the registered patients were males (516, 52.4%). In terms of TB types, 381 (38.7%), 241 (24.5%), and 363 (36.9%) patients had smear-negative pulmonary TB, smear-positive pulmonary TB, and extra pulmonary TB, respectively. Six hundred and seventy-two patients (90.1%) had successful treatment outcomes (cured and treatment completed), while 74 patients (9.9%) had unsuccessful treatment outcomes (death and treatment failure).TB treatment outcome was not associated with age, sex, type and history of TB, or co-infection with HIV (P > 0.05). The proportion of TB/HIV co-infection was at 24.2%, and these were found to be significantly associated with the age groups of 25-34, 35-44 and ≥65 years:(aOR: 0.44; 95% CI: 0.25-0.8), (aOR: 0.39; 95% CI: 0.20-0.70), (aOR: 4.2; 95% CI: 1.30-12.9), respectively.

CONCLUSIONS

The proportion of patients with successful treatment outcomes was above the World Health Organization target set for Millennium Development Goal of 85% and in line with that of the global milestone target set at > 90% for 2025. Relatively higher proportions of transfer-out cases were recorded in the present study. Similarly, the proportion of TB/HIV co-infection cases was much higher than the national average of 8%.Thus, the health facility under study should develop strategies to record the final treatment outcome of transfer-out cases. In addition, strategies to reduce the burden of TB/HIV co-infection should be strengthened.

The IL20 Genetic Polymorphism Is Associated with Altered Clinical Outcome in Septic Shock

BACKGROUND

The IL10 family of genes includes crucial immune regulators. We tested the hypothesis that single nucleotide polymorphisms (SNPs) in IL10, IL19, IL20, and IL24 of the IL10 family gene cluster alter the clinical outcome of septic shock.

METHODS

Patients with septic shock (n = 1,193) were genotyped for 13 tag SNPs of IL10, IL19, IL20, and IL24. IL20 gene expression was measured in genotyped lymphoblastoid cells in vitro. Cardiac surgical ICU patients (n = 981) were genotyped for IL20 rs2981573 A/G. The primary outcome variable was 28-day mortality.

RESULTS

Patients with the G allele of IL20 rs2981573 had a significantly increased hazard of death over the 28-day period compared to patients with the A allele in the septic shock cohort (adjusted hazard ratio 1.27; 95% confidence interval 1.10-1.47; p = 8.0 × 10-4). Patients with the GG genotype had more organ dysfunction (p < 0.05). The GG genotype was associated with increased IL20 gene expression in stimulated lymphoblastoid cells in vitro (p < 0.05). The cardiac surgical ICU patients with the GG genotype had an increased length of ICU stay (p = 0.032).

CONCLUSIONS

The GG genotype of IL20 rs2981573 SNP was associated with increased IL20 gene expression and increased adverse outcomes in patients with septic shock and following cardiac surgery.

Maternal sepsis in the era of genomic medicine

PURPOSE

Maternal sepsis remains one of the leading causes of direct and indirect maternal mortality both in high- and low-income environments. In the last two decades, systems biology approaches, based on '-omics' technologies, have started revolutionizing the diagnosis and management of the septic syndrome. The scope of this narrative review is to present an overview of the basic '-omics' technologies, exemplified by cases relevant to maternal sepsis.

METHODS

Narrative review of the new '-omics' technologies based on a detailed review of the literature.

RESULTS

After presenting the main 'omics' technologies, we discuss their limitations and the need for integrated approaches that encompass research efforts across multiple '-omics' layers in the '-omics' cascade between the genome and the phenome.

CONCLUSIONS

Systems biology approaches are revolutionizing the research landscape in maternal sepsis. There is a need for increased awareness, from the side of health practitioners, as a requirement for the effective implementation of the new technologies in the research and clinical practice in maternal sepsis.

Gene-Environment Interaction in the Intergenerational Transmission of Asthma

Researchers have found strong linkages between parent and child health, but the mechanisms underlying intergenerational health transmission are not well understood. This paper investigates how the importance of genetic health transmission mechanisms varies by environmental conditions in the case of pediatric asthma, the single most common chronic health condition among American children. Using a sample that includes approximately 2000 adoptees and a large number of similar biological families, I find that the relative importance of genetic transmission differs strongly by socioeconomic status (SES). In high SES families, parent-child asthma associations are approximately 75% weaker among adoptees than biological children, suggesting a dominant role for genetic transmission. In lower SES families, parent-child asthma associations are virtually identical across biological and adoptive children, suggesting a negligible role for genetic transmission. A potential interpretation of this difference is that as environmental conditions affecting asthma improve among higher SES children, an increasingly large share of asthma variation is due to genetics. Copyright © 2016 John Wiley & Sons, Ltd.

Clinical relevance of peroxisome proliferator-activated receptor-γ gene polymorphisms with sepsis

BACKGROUND

Peroxisome proliferator-activated receptor-γ (PPARγ) is a regulator of inflammation. This study aimed to explore associations between PPARγ gene single-nucleotide polymorphisms (SNPs) and susceptibility to and clinical outcome of sepsis in the North China Han population.

METHODS

This study included 303 patients with sepsis and 303 controls. We conducted genetic typing for 13 common PPARγ gene SNPs (improved multiplex ligation detection reaction), linkage disequilibrium mapping, and haplotype inference. Associations between SNP genotypes/haplotypes and sepsis susceptibility and outcome (septic shock, organ dysfunction, or death) were assessed using unconditional logistic regression analysis.

RESULTS

For rs2972164, patients with genotypes CT/CT+TT had higher risk of sepsis than genotype CC (odds ratio [95% CI]: 1.74 [1.05-2.86], P = .03 and 1.72 [1.06-2.80], P = .026, respectively); the T allele was associated with increased sepsis risk compared with the C allele (1.64 [1.04-2.58], P = .033). For rs1801282, genotypes CG/CG+GG had lower risk of sepsis than genotype CC (0.55 [0.33-0.92], P = .024 and 0.57 [0.35-0.95], P = .03, respectively); the G allele was associated with decreased sepsis risk compared with the C allele (0.62 [0.39-1.01], P = .055). For rs4135275, genotypes AG/AG+GG had higher risk of severe organ dysfunction (multiple organ dysfunction syndrome score >8) than genotype AA (2.66 [1.16-6.09], P = .038 and 2.21 [1.00-4.85], P = .042, respectively). Haplotype TAT (rs2972164, rs4684846, and rs17036188) was associated with increased sepsis risk (1.66 [1.03-2.67], P = .038).

CONCLUSIONS

No mutation was correlated with septic shock or death. PPARγ gene polymorphisms may play a role in the occurrence and progression of sepsis in the North China Han population.

Genome-wide association study of sepsis in extremely premature infants

OBJECTIVE

To identify genetic variants associated with sepsis (early-onset and late-onset) using a genome-wide association (GWA) analysis in a cohort of extremely premature infants.

STUDY DESIGN

Previously generated GWA data from the Neonatal Research Network's anonymised genomic database biorepository of extremely premature infants were used for this study. Sepsis was defined as culture-positive early-onset or late-onset sepsis or culture-proven meningitis. Genomic and whole-genome-amplified DNA was genotyped for 1.2 million single-nucleotide polymorphisms (SNPs); 91% of SNPs were successfully genotyped. We imputed 7.2 million additional SNPs. p Values and false discovery rates (FDRs) were calculated from multivariate logistic regression analysis adjusting for gender, gestational age and ancestry. Target statistical value was p<10-5. Secondary analyses assessed associations of SNPs with pathogen type. Pathway analyses were also run on primary and secondary end points.

RESULTS

Data from 757 extremely premature infants were included: 351 infants with sepsis and 406 infants without sepsis. No SNPs reached genome-wide significance levels (5×10-8); two SNPs in proximity to FOXC2 and FOXL1 genes achieved target levels of significance. In secondary analyses, SNPs for ELMO1, IRAK2 (Gram-positive sepsis), RALA, IMMP2L (Gram-negative sepsis) and PIEZO2 (fungal sepsis) met target significance levels. Pathways associated with sepsis and Gram-negative sepsis included gap junctions, fibroblast growth factor receptors, regulators of cell division and interleukin-1-associated receptor kinase 2 (p values<0.001 and FDR<20%).

CONCLUSIONS

No SNPs met genome-wide significance in this cohort of extremely low birthweight infants; however, areas of potential association and pathways meriting further study were identified.

Human Genetic Determinants of Viral Diseases

Much progress has been made in the identification of specific human gene variants that contribute to enhanced susceptibility or resistance to viral diseases. Herein we review multiple discoveries made with genome-wide or candidate gene approaches that have revealed significant insights into virus-host interactions. Genetic factors that have been identified include genes encoding virus receptors, receptor-modifying enzymes, and a wide variety of innate and adaptive immunity-related proteins. We discuss a range of pathogenic viruses, including influenza virus, respiratory syncytial virus, human immunodeficiency virus, human T cell leukemia virus, human papilloma virus, hepatitis B and C viruses, herpes simplex virus, norovirus, rotavirus, parvovirus, and Epstein-Barr virus. Understanding the genetic underpinnings that affect infectious disease outcomes should allow tailored treatment and prevention approaches in the future.

The role of human host genetics in tuberculosis resistance

INTRODUCTION

Tuberculosis (TB) remains a public health problem: the latest estimate of new incident cases per year is a staggering 10.4 million. Despite this overwhelming number, the majority of the immunocompetent population can control infection with Mycobacterium tuberculosis. The human genome underlies the immune response and contributes to the outcome of TB infection. Areas covered: Investigations of TB resistance in the general population have closely mirrored those of other infectious diseases and initially involved epidemiological observations. Linkage and association studies, including studies of VDR, SLC11A1 and HLA-DRB1 followed. Genome-wide association studies of common variants, not necessarily sufficient for disease, became possible after technological advancements. Other approaches involved the identification of those individuals with rare disease-causing mutations that strongly predispose to TB, epistasis and the role of ethnicity in disease. Despite these efforts, infection outcome, on an individual basis, cannot yet be predicted. Expert commentary: The early identification of future disease progressors is necessary to stem the TB epidemic. Human genetics may contribute to this endeavour and could in future suggest pathways to target for disease prevention. This will however require concerted efforts to establish large, well-phenotyped cohorts from different ethnicities, improved genomic resources and a better understanding of the human genome architecture.

Treatable traits and therapeutic targets: Goals for systems biology in infectious disease

Among the many medical applications of systems biology, we contend that infectious disease is one of the most important and tractable targets. We take the view that the complexity of the immune system is an inevitable consequence of its evolution, and this complexity has frustrated reductionist efforts to develop host-directed therapies for infection. However, since hosts vary widely in susceptibility and tolerance to infection, host-directed therapies are likely to be effective, by altering the biology of a susceptible host to induce a response more similar to a host who survives. Such therapies should exert minimal selection pressure on organisms, thus greatly decreasing the probability of pathogen resistance developing.

A systems medicine approach to infection has the potential to provide new solutions to old problems: to identify host traits that are potentially amenable to therapeutic intervention, and the host immune factors that could be targeted by host-directed therapies. Furthermore, undiscovered sub-groups with different responses to treatment are almost certain to exist among patients presenting with life-threatening infection, since this population is markedly clinically heterogeneous. A major driving force behind high-throughput clinical phenotyping studies is the aspiration that these subgroups, hitherto opaque to observation, may be observed in the data generated by new technologies. Subgroups of patients are unlikely to be static – serial clinical and biological phenotyping may reveal different trajectories through the pathophysiology of disease, in which different therapeutic approaches are required.

We suggest there are two major goals for systems biology in infection medicine: (1) to identify subgroups of patients that share treatable features; and, (2) to integrate high-throughput data from clinical and in vitro sources in order to predict tractable therapeutic targets with the potential to alter disease trajectories for individual patients.

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High throughput technologies can reveal clinical patterns in infection that were previously opaque.

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Host-targeted therapies have conceptual advantages but are difficult to develop.

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Key clinically-relevant objectives are identification of disease endotypes and treatable traits.

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Mechanistic understanding will reveal opportunities for drug design, repurposing and better targeting.

A path to precision in the ICU

Precision medicine is increasingly touted as a groundbreaking new paradigm in biomedicine. In the ICU, the complexity and ambiguity of critical illness syndromes have been identified as fundamental justifications for the adoption of a precision approach to research and practice. Inherently protean diseases states such as sepsis and acute respiratory distress syndrome have manifestations that are physiologically and anatomically diffuse, and that fluctuate over short periods of time. This leads to considerable heterogeneity among patients, and conditions in which a “one size fits all” approach to therapy can lead to widely divergent results. Current ICU therapy can thus be seen as imprecise, with the potential to realize substantial gains from the adoption of precision medicine approaches. A number of challenges still face the development and adoption of precision critical care, a transition that may occur incrementally rather than wholesale. This article describes a few concrete approaches to addressing these challenges.

First, novel clinical trial designs, including registry randomized controlled trials and platform trials, suggest ways in which conventional trials can be adapted to better accommodate the physiologic heterogeneity of critical illness. Second, beyond the “omics” technologies already synonymous with precision medicine, the data-rich environment of the ICU can generate complex physiologic signatures that could fuel precision-minded research and practice. Third, the role of computing infrastructure and modern informatics methods will be central to the pursuit of precision medicine in the ICU, necessitating close collaboration with data scientists. As work toward precision critical care continues, small proof-of-concept studies may prove useful in highlighting the potential of this approach.

Enhanced understanding of the host-pathogen interaction in sepsis: new opportunities for omic approaches

Progress in sepsis research has been severely hampered by a heterogeneous disease phenotype, limiting the interpretation of clinical trials and the development of effective therapeutic interventions. Application of omics-based methodologies is advancing understanding of the dysregulated host immune response to infection in sepsis. However, the frequently elusive nature of the infecting organism in sepsis has limited efforts to understand the effect of disease heterogeneity involving the pathogen. Recent advances in nucleic acid sequencing-based pathogen analysis provide the opportunity for more accurate and comprehensive microbiological diagnosis. In this Review, we explore how better understanding of the host-pathogen interaction can substantially enhance, and in turn benefit from, current and future application of omics-based approaches to understand the host response in sepsis. We illustrate this using recent work accounting for heterogeneity involving the pathogen. We propose that there is a timely opportunity to further resolve sepsis heterogeneity by considering host-pathogen interactions, enabling progress towards a precision medicine approach.

Human immune system variation

The human immune system is highly variable between individuals but relatively stable over time within a given person. Recent conceptual and technological advances have enabled systems immunology analyses, which reveal the composition of immune cells and proteins in populations of healthy individuals. The range of variation and some specific influences that shape an individual's immune system is now becoming clearer. Human immune systems vary as a consequence of heritable and non-heritable influences, but symbiotic and pathogenic microbes and other non-heritable influences explain most of this variation. Understanding when and how such influences shape the human immune system is key for defining metrics of immunological health and understanding the risk of immune-mediated and infectious diseases.

Molecular Mechanisms of Prothrombotic Risk Due to Genetic Variations in Platelet Genes: Enhanced Outside-In Signaling Through the Pro33 Variant of Integrin β3

In recent years inherited variations in platelet proteins have emerged as potential risk factors that could predispose individuals to arterial thrombosis. Although many studies have examined the association of platelet gene polymorphisms with particular disease states, the underlying mechanisms by which most of these polymorphisms contribute to the pathophysiology of thrombosis have remained largely unexplored. This review will focus on the cellular and molecular features by which these genetic changes affect platelet physiology. Although many genes have been investigated in this regard, only the genes encoding integrins β3 and α2, and the platelet Fc receptor, FcγRIIA, have been studied in any depth. In some cases (such as integrin α2), evidence supports a quantitative trait locus. For other genes, nonsynonymous nucleotide substitutions lead to structural and functional consequences. A large portion of this review will focus on the widely studied Leu33Pro (PIA) polymorphism of integrin β3, and will consider the potential mechanisms by which the Pro33 polymorphism could induce a prothrombotic risk. A detailed understanding of how polymorphisms modulate platelet physiology will be important for understanding individual differences in response to antiplatelet therapy.