Mobile genes in the human microbiome are structured from global to individual scales.

Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. Notably, we also observed differences between the mobile gene pools of neighbouring Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviours provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important for colonizing specific human populations.

A Nationwide Retrospective Analysis of Out-of-Hospital Pediatric Cardiopulmonary Resuscitation Treated by Helicopter Emergency Medical Service in the Netherlands.

OBJECTIVE: There is generally limited but conflicting literature on the incidence, causes, and outcomes of pediatric out-of-hospital cardiac arrest. This study was performed to determine the incidence and outcome of pediatric out-of-hospital cardiac arrest reported by all helicopter emergency medical services in the Netherlands and to provide a description of causes and treatments and, in particular, a description of the specific interventions that can be performed by a physician-staffed helicopter emergency medical service. METHODS: A retrospective analysis was performed of all documented pediatric (0 < 18 years of age) out-of-hospital cardiac arrests from July 2015 to July 2017, attended by all 4 Dutch helicopter emergency medical service teams. RESULTS: Two hundred two out-of-hospital cardiac arrests were identified. The overall incidence in the Netherlands is 3.5 out-of-hospital cardiac arrests in children per 100,000 pediatric inhabitants. The overall survival rate for out-of-hospital cardiac arrest was 11.4%. Eleven (52%) of the survivors were in the drowning group and between 12 and 96 months of age. CONCLUSION: Helicopter emergency medical services are frequently called to pediatric out-of-hospital cardiac arrests in the Netherlands. The survival rate is normal to high compared with other countries. The 12- to 96-month age group and drowning seem to have a relatively favorable outcome.

Prehospital Management of Peripartum Neonatal Complications by Helicopter Emergency Medical Service in the South West of the Netherlands: An Observational Study.

OBJECTIVE: Emergency medical service (EMS) is responsible for prehospital care encompassing all ages, irrespective of injury cause or medical condition, which includes peripartum emergencies. When patients require care more advanced than the level provided by the national EMS protocol, an EMS physician-staffed Dutch helicopter emergency medical service (HEMS) may be dispatched. In the Netherlands in 2016, there were 21.434 planned home births guided by midwives alone without further obstetric assistance, accounting for 12.7% of all births that year. However, there are no clear data available thus far regarding neonates requiring emergency care with or without HEMS assistance. This article reviews neonates during our study period who received medical care after birth by HEMS. METHODS: A retrospective chart review was performed including neonates born on the day of the dispatch between January 2012 and December 2017 who received additional medical care from the Rotterdam HEMS. RESULTS: Fifty-two neonates received medical care by HEMS. The majority (73.1%) were full-term (Gestational age > 37 weeks). Home delivery was intended in 63.5%, 20% of whom experienced an uncomplicated delivery but had a poor start of life. The majority of unplanned deliveries (n = 17) were preterm (70.6%). Two were born by resuscitative hysterotomy; 1 survived in good neurologic condition, and the other died at the scene. Fifteen neonates (28.9%) required cardiopulmonary resuscitation; in 2 cases, no resuscitation was started on medical grounds, and 12 of the other 13 resuscitated neonates regained return of spontaneous circulation. In 33 (63.5%) of the neonates, respiratory interventions were required; 8 (15.4%) were intubated before transport. Death was confirmed in 5 (9.6%) neonates, all preterm. CONCLUSION: During the study period, 52 neonates required medical assistance by HEMS. The 5 infants who died were all preterm. In this cohort, adequate basic life support was implemented immediately after birth either by the attending midwife, EMS, or HEMS on arrival. This suggests that prehospital first responders know the basic skills of neonatal life support.

Succinate is an inflammatory signal that induces IL-1ß through HIF-1α.

Macrophages activated by the Gram-negative bacterial product lipopolysaccharide switch their core metabolism from oxidative phosphorylation to glycolysis. Here we show that inhibition of glycolysis with 2-deoxyglucose suppresses lipopolysaccharide-induced interleukin-1ß but not tumour-necrosis factor-α in mouse macrophages. A comprehensive metabolic map of lipopolysaccharide-activated macrophages shows upregulation of glycolytic and downregulation of mitochondrial genes, which correlates directly with the expression profiles of altered metabolites. Lipopolysaccharide strongly increases the levels of the tricarboxylic-acid cycle intermediate succinate. Glutamine-dependent anerplerosis is the principal source of succinate, although the 'GABA (γ-aminobutyric acid) shunt' pathway also has a role. Lipopolysaccharide-induced succinate stabilizes hypoxia-inducible factor-1α, an effect that is inhibited by 2-deoxyglucose, with interleukin-1ß as an important target. Lipopolysaccharide also increases succinylation of several proteins. We therefore identify succinate as a metabolite in innate immune signalling, which enhances interleukin-1ß production during inflammation.

A Physician-Based Helicopter Emergency Medical Services Was Associated With an Additional 2.5 Lives Saved per 100 Dispatches of Severely Injured Pediatric Patients.

OBJECTIVE: Physician-based helicopter emergency medical services (HEMS) provide specialist medical care to the accident scene in order to improve the survival of severely injured patients. Studies that focus on the role of physician-based HEMS in pediatric trauma are scarce. The aim of this retrospective, observational study was to determine the effect of physician-based HEMS assistance on the survival of severely injured pediatric patients. METHODS: All consecutive severely injured pediatric patients (age < 18 years and Injury Severity Score > 15) treated between October 1, 2000, and February 28, 2013, were included. The survival of patients who received medical care of physician-based HEMS was compared with the survival of patients treated by an ambulance paramedic crew (ie, emergency medical services group) only. A regression model was developed for calculating the survival benefit in the physician-based HEMS group. RESULTS: A total of 308 patients were included; 112 (36%) were primarily treated by emergency medical services, and 196 (64%) patients received additional physician-based HEMS assistance on scene. The model with the best diagnostic properties and fit contained physician-based HEMS assistance, 3 components of the Glasgow Coma Scale (eye, motor, and verbal) scored prehospitally (before intubation), ordinal values for the Injury Severity Scale, systolic blood pressure, and respiratory rate. This model predicted that 5 additional patients survived because of physician-based HEMS assistance. This corresponds with 2.5 additional lives saved per 100 physician-based HEMS dispatches for severely injured pediatric patients. CONCLUSION: The data suggest that an additional 2.5 lives might be saved per 100 physician-based HEMS dispatches for severely injured pediatric patients.

Prehospital Blood Transfusions in Pediatric Patients by a Helicopter Emergency Medical Service.

OBJECTIVE: In the prehospital setting, the Nijmegen and Rotterdam helicopter emergency medical services administer packed red blood cells to critically ill or injured pediatric patients. Blood is given on scene or during transport and is derived from nearby hospitals. We summarize our experience with prehospital blood use in pediatric patients. METHODS: The databases from both the Nijmegen and Rotterdam helicopter emergency medical services were reviewed for all pediatric (< 18 years) patients who received packed red blood cells on scene or during transport to the hospital. RESULTS: Between 2007 and 2015, 10 pediatric patients out of approximately 2,400 pediatric patients received blood in the prehospital setting. The median Injury Severity Score was 41. Seven hospitals delivered blood in the prehospital setting at the scene. All patients were in hypovolemic shock. Two patients died. Two patients were believed to be unexpected survivors; 1 was predicted by the Trauma and Injury Severity Score, and a second unexpected survivor was a neonate who was in hypovolemic shock and cardiopulmonary arrest. CONCLUSION: The incidence of prehospital use of blood in injured or critically ill children is low. This intervention presented a potential to limit acid-base disturbance, low hemoglobin levels, and coagulopathy in this group. We believe this cohort also contains 2 unexpected survivors.

Autophagy is redundant for the host defense against systemic Candida albicans infections.

Autophagy has been demonstrated to play an important role in the immunity against intracellular pathogens, but very little is known about its role in the host defense against fungal pathogens such as Candida albicans. Therefore, the role of autophagy for the host defense against C. albicans was assessed by complementary approaches using mice defective in autophagy, as well as immunological and genetic studies in humans. Although C. albicans induced LC3-II formation in macrophages, myeloid cell-specific ATG7(-/-) mice with defects in autophagy did not display an increased susceptibility to disseminated candidiasis. In in vitro experiments in human blood mononuclear cells, blocking autophagy modulated cytokine production induced by lipopolysaccharide, but not by C. albicans. Furthermore, autophagy modulation in human monocytes did not influence the phagocytosis and killing of C. albicans. Finally, 18 single-nucleotide polymorphisms in 13 autophagy genes were not associated with susceptibility to candidemia or clinical outcome of disease in a large cohort of patients, and there was no correlation between these genetic variants and cytokine production in either candidemia patients or healthy controls. Based on these complementary in vitro and in vivo studies, it can be concluded that autophagy is redundant for the host response against systemic infections with C. albicans.

Procedural sedation by advanced practice providers in the emergency medical service in the Netherlands: a retrospective study.

BACKGROUND: Procedural sedation and analgesia (PSA) is a technique of administering sedatives to induce a state that allows the patient to tolerate painful procedures while maintaining cardiorespiratory function, a condition that is frequently desired prehospital. Non-physician prehospital clinicians often have a limited scope of practice when it comes to providing analgesia and sedation; sometimes resulting in a crew request for back-up from physician-staffed prehospital services.". This is also the case if sedation is desirable. Advanced practice providers (APPs), who are legally authorized and trained to carry out this procedure, may be a solution when the physician-staffed service is not available or will not be available in time. METHODS: The aim of this study is to gain insight in the circumstances in which an APP, working at the Dutch ambulance service "RAV Brabant MWN" from January 2019 to December 2022, uses propofol for PSA or to provide sedation. With this a retrospective observational document study we describe the characteristics of patients and ambulance runs and evaluates the interventions in terms of safety. RESULTS: During the study period, the APPs administered propofol 157 times for 135 PSA and in 22 cases for providing sedation. The most common indication was musculoskeletal trauma such as fracture care or the reduction of joint dislocation. In 91% of the situations where propofol was used, the predetermined goal e.g. alignment of fractured extremity, repositioning of luxated joint or providing sedation the goal was achieved. There were 12 cases in which one or more adverse events were documented and all were successfully resolved by the APP. There were no cases of laryngospam, airway obstruction, nor anaphylaxis. None of the adverse events led to unexpected hospitalization or death. CONCLUSION: During the study period, the APPs performed 135 PSAs and provided 22 sedations. The success rate of predetermined goals was higher than that stated in the literature. Although there were a number of side effects, their incidences were lower than those reported in the literature, and these were resolved by the APP during the episode of care. Applying a PSA by an APP at the EMS "RAV Brabant MWN" appears to be safe with a high success rate.

Unravelling the pathogenesis of inflammatory bowel disease.

Recently, substantial advances in the understanding of the molecular pathogenesis of inflammatory bowel disease (IBD) have been made owing to three related lines of investigation. First, IBD has been found to be the most tractable of complex disorders for discovering susceptibility genes, and these have shown the importance of epithelial barrier function, and innate and adaptive immunity in disease pathogenesis. Second, efforts directed towards the identification of environmental factors implicate commensal bacteria (or their products), rather than conventional pathogens, as drivers of dysregulated immunity and IBD. Third, murine models, which exhibit many of the features of ulcerative colitis and seem to be bacteria-driven, have helped unravel the pathogenesis/mucosal immunopathology of IBD.

A survey of the current nurse practitioner and physician assistant workforce in Dutch ambulance care.

Background: Dutch ambulance service faces future challenges due to acute care development, patient changes, demographics, increased ambulance runs and regional differences. Ambulance Care Netherlands published a framework titled "Pilot physician assistant and nurse practitioner ambulance care". Within this framework, a role is proposed so that their qualifications can provide solutions to future challenges. Despite the introduction of nurse practitioners and physician assistants into Dutch ambulance care, little is known about the effects of this introduction or the tasks these professionals perform. Nevertheless, they are being called upon, even though it is not known whether their potential contribution to the desired outcome described in the framework. Objective: This study aims to provide an overview of all nurse practitioners and physician assistants working in Dutch ambulance care and the tasks they perform. Design: We used a cross-sectional exploratory study design. The nurse practitioners and physician assistants participated in a structured telephone survey. Setting: Emergency ambulance services in the Netherlands. Participants: A total of 56 respondents participated in a telephone survey. Results: We found 53 nurse practitioners and 20 physician assistants working in Dutch ambulance care, 56 participated in the survey. Their performance of both direct care and indirect care tasks differed considerably. While some nurse practitioners and physician assistants were fully autonomous in-patient care, others were bound by regulations and restrictions. Conclusions: We found large variations between respondents in direct and indirect care task, number of working hours, and the different positions within the different Emergency ambulance services in the Netherlands. As a result, the established framework cannot presently function but can provide sound guidance to different ambulance services in positioning their nurse practitioners or physician assistants.

Exploring the interplay of barrier function and leukocyte recruitment in intestinal inflammation by targeting fucosyltransferase VII and trefoil factor 3.

Intestinal mucosal integrity is dependent on epithelial function and a regulated immune response to injury. Fucosyltransferase VII (Fuc-TVII) is an essential enzyme required for the expression of the functional ligand for E- and P-selectin. Trefoil factor 3 (TFF3) is involved in both protecting the intestinal epithelium against injury as well as aiding in wound repair following injury. The aim of the present study was to assess the interplay between barrier function and leukocyte recruitment in intestinal inflammation. More specifically, we aimed to examine how targeted disruption of Fuc-TVII either in wild-type or TFF3(-/-) mice would alter their susceptibility to colonic injury. TFF3 and Fuc-TVII double-knockout mice (TFF3/Fuc-TVII(-/-) mice) were generated by mating TFF3(-/-) and Fuc-TVII(-/-) mice. Colitis was induced by administration of dextran sodium sulfate (DSS) (2.5% wt/vol) in the drinking water. Changes in baseline body weight, diarrhea, and fecal blood were assessed daily. Upon euthanasia, extents of colonic inflammation were assessed macroscopically, microscopically, and through quantification of myeloperoxidase (MPO) activity. Colonic lymphocyte subpopulations were assessed at 6 days after administration of DSS by flow cytometry and immunohistochemistry. No baseline intestinal inflammation was found in TFF3/Fuc-TVII(-/-), TFF3(-/-), Fuc-TVII(-/-), or wild-type mice. Loss of Fuc-TVII resulted in a reduction in disease severity whereas TFF3(-/-) mice were markedly more susceptible to DSS-induced colitis. Remarkably, the loss of Fuc-TVII in TFF3(-/-) mice markedly decreased the severity of DSS-induced colitis as evidenced by reduced weight loss, diarrhea, decreased colonic MPO levels and improved survival. Furthermore, the loss of TFF3 resulted in increased severity of spontaneous colitis in IL-2/beta-microglobulin-deficient mice. These studies highlight the importance of the interplay between factors involved in the innate immune response, mucosal barrier function, and genes involved in regulating leukocyte recruitment and other aspects of the immune response.

Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis.

OBJECTIVES: Genetic susceptibility is known to play a large part in the predisposition to the inflammatory bowel diseases (IBDs) known as Crohn's disease (CD) and ulcerative colitis (UC). The IL2/IL21 locus on 4q27 is known to be a common risk locus for inflammatory disease (shown in coeliac disease, type 1 diabetes, rheumatoid arthritis, systemic lupus erythematosus and psoriasis), while the roles that interleukin 2 (IL2) and IL21 play in the immune response also make them attractive candidates for IBD. The objective of this study was to test for association between the IL2/IL21 locus and the IBDs. METHODS: The four single nucleotide polymorphisms (SNPs) in the IL2/IL21 locus most associated with coeliac disease were genotyped in 1590 subjects with IBD and 929 controls from The Netherlands, and then replicated in a North American cohort (2387 cases and 1266 controls) and an Italian cohort (805 cases and 421 controls), yielding a total of 4782 cases (3194 UC, 1588 CD) and 2616 controls. Allelic association testing and a pooled analysis using a Cochran-Mantel-Haenszel test were performed. RESULTS: All four SNPs were strongly associated with UC in all three cohorts and reached genome-wide significance in the pooled analysis (rs13151961 p = 1.35 x 10(-10), rs13119723 p = 8.60 x 10(-8), rs6840978 p = 3.0 7x 10(-8), rs6822844 p = 2.77 x 10(-9)). A moderate association with CD was also found in the pooled analysis (p value range 0.0016-9.86 x 10(-5)). CONCLUSIONS: A strong association for the IL2/IL21 locus with UC was found, which also confirms it as a general susceptibility locus for inflammatory disease.

Microbiology. How to get along--friendly microbes in a hostile world.

Microbiologists have long been puzzled by the finding that the gut mucosa does not respond to the myriad varieties of bacteria that normally reside in the gut. As Xavier and Podolsky explain in their Perspective, this may be because bacteria that are indigenous to the gut have learned ways to switch off pathways in gut epithelial cells that lead to switching on of genes involved in inflammation (Neish et al.).

Correction: Intestinal epithelial cell-specific RARα depletion results in aberrant epithelial cell homeostasis and underdeveloped immune system.

The original version of this Article omitted the author Margarita Parada-kusz from the Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.

Are on-scene blood transfusions by a helicopter emergency medical service useful and safe? A multicentre case-control study.

INTRODUCTION: In the prehospital setting, crystalloid fluids are frequently used, but only erythrocytes are capable of transporting oxygen to tissues. The aim of this study was to establish the efficacy and safety of the prehospital use of uncross matched type O rhesus-negative packed red blood cells (URBC) by the Dutch physician-staffed helicopter emergency medical service. We hypothesized that prehospital URBC transfusions are safe and more effective with respect to survival than resuscitations with crystalloids. METHODS: The effects of prehospital URBC transfusions were studied by comparing a cohort of patients (>18 years) who were treated with a combination of URBC and crystalloid fluids with a matched control group of patients who received crystalloid fluids alone. RESULTS: Among 73 adults who received prehospital URBC transfusions, 50 (68%) patients were included. No transfusion reactions were observed. No effect of prehospital transfusion on 24-h or 30-day survival was found. Haemoglobin levels at presentation to the emergency department were higher in the URBC cohort. The two groups had similar cumulative erythrocyte requirements within the first 24 h. CONCLUSION: Neither survival benefits nor a decreased incidence of shock on admission were observed after prehospital helicopter emergency medical service URBC transfusions. There were no prehospital transfusion reactions in this study; therefore, URBC transfusions were deemed to be safe. A prospective randomized study is warranted to evaluate the effect of early URBC transfusions and transfusions with preheated URBC on the survival of patients with severe prehospital haemorrhagic shock.

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research.

Our understanding of how the gut microbiome interacts with its human host has been restrained by limited access to longitudinal datasets to examine stability and dynamics, and by having only a few isolates to test mechanistic hypotheses. Here, we present the Broad Institute-OpenBiome Microbiome Library (BIO-ML), a comprehensive collection of 7,758 gut bacterial isolates paired with 3,632 genome sequences and longitudinal multi-omics data. We show that microbial species maintain stable population sizes within and across humans and that commonly used 'omics' survey methods are more reliable when using averages over multiple days of sampling. Variation of gut metabolites within people over time is associated with amino acid levels, and differences across people are associated with differences in bile acids. Finally, we show that genomic diversification can be used to infer eco-evolutionary dynamics and in vivo selection pressures for strains within individuals. The BIO-ML is a unique resource designed to enable hypothesis-driven microbiome research.

MAST3: a novel IBD risk factor that modulates TLR4 signaling.

Inflammatory bowel disease (IBD) is a chronic disorder caused by multiple factors in a genetically susceptible host. Significant advances in the study of genetic susceptibility have highlighted the importance of the innate immune system in this disease. We previously completed a genome-wide linkage study and found a significant locus (IBD6) on chromosome 19p. We were interested in identifying the causal variant in IBD6. We performed a two-stage association mapping study. In stage 1, 1530 single-nucleotide polymorphisms (SNPs) were selected from the HapMap database and genotyped in 761 patients with IBD. Among the SNPs that passed the threshold for replication, 26 were successfully genotyped in 754 additional patients (stage 2). One intronic variant, rs273506, located in the microtubule-associated serine/threonine-protein kinase gene-3 (MAST3), was found to be associated in both stages (pooled P=1.8 x 10(-4)). We identified four MAST3 coding variants, including a non-synonymous SNP rs8108738, correlated to rs273506 and associated with IBD. To test whether MAST3 was expressed in cells of interest, we performed expression assays, which showed abundant expression of MAST3 in antigen-presenting cells and in lymphocytes. The knockdown of MAST3 specifically decreased Toll-like receptor-4-dependent NF-kappaB activity. Our findings are additional proofs of the pivotal role played by modulators of NF-kappaB activity in IBD pathogenesis.

Helminth-induced alterations of the gut microbiota exacerbate bacterial colitis.

Infection with the intestinal helminth parasite Heligmosomoides polygyrus exacerbates the colitis caused by the bacterial enteropathogen Citrobacter rodentium. To clarify the underlying mechanism, we analyzed fecal microbiota composition of control and helminth-infected mice and evaluated the functional role of compositional differences by microbiota transplantation experiments. Our results showed that infection of Balb/c mice with H. polygyrus resulted in significant changes in the composition of the gut microbiota, characterized by a marked increase in the abundance of Bacteroidetes and decreases in Firmicutes and Lactobacillales. Recipients of the gut microbiota from helminth-infected wide-type, but not STAT6-deficient, Balb/c donors had increased fecal pathogen shedding and significant worsening of Citrobacter-induced colitis compared to recipients of microbiota from control donors. Recipients of helminth-altered microbiota also displayed increased regulatory T cells and IL-10 expression. Depletion of CD4+CD25+ T cells and neutralization of IL-10 in recipients of helminth-altered microbiota led to reduced stool C. rodentium numbers and attenuated colitis. These results indicate that alteration of the gut microbiota is a significant contributor to the H. polygyrus-induced exacerbation of C. rodentium colitis. The helminth-induced alteration of the microbiota is Th2-dependent and acts by promoting regulatory T cells that suppress protective responses to bacterial enteropathogens.