References 1 Carapetis JR, Jacoby P, Carville K, Joel Ang SJ, Curtis N, Andrews R Effectiveness of clindamycin and intravenous immunoglobulin, and risk of disease in contacts, in invasive group a stre[.]
e1 References Carapetis JR, Jacoby P, Carville K, Joel Ang SJ, Curtis N, Andrews R Effectiveness of clindamycin and intravenous immunoglobulin, and risk of disease in contacts, in invasive group a streptococcal infections Clin Infect Dis 2014;59:358-365 Parks T, Wilson C, Curtis N, Norrby-Teglund A, Sriskandan S Polyspecific intravenous immunoglobulin in clindamycin-treated patients with streptococcal toxic shock syndrome: a systematic review and meta-analysis Clin Infect Dis 2018;67:1434-1436 Balkhi MY, Ma Q, Ahmad S, Junghans RP T cell exhaustion and interleukin downregulation Cytokine 2015;71:339-347 Guignant C, Lepape A, Huang X, et al Programmed death-1 levels correlate with increased mortality, nosocomial infection and immune dysfunctions in septic shock patients Crit Care 2011;15:R99 Boomer JS, To K, Chang KC, et al Immunosuppression in patients who die of sepsis and multiple organ failure JAMA 2011;306:25942605 Fallon EA, Biron-Girard BM, Chung CS, et al A novel role for coinhibitory receptors/checkpoint proteins in the immunopathology of sepsis J Leukoc Biol 2018 Epub ahead of print Becattini S, Latorre D, Mele F, et al T cell immunity Functional heterogeneity of human memory CD4(1) T cell clones primed by pathogens or vaccines Science 2015;347:400-406 Geginat J, Paroni M, Maglie S, et al Plasticity of human CD4 T cell subsets Front Immunol 2014;5:630 Mai J, Wang H, Yang XF Th 17 cells interplay with Foxp31 Tregs in regulation of inflammation and autoimmunity Front Biosci 2010;15:986-1006 10 Romagnani S, Maggi E, Liotta F, Cosmi L, Annunziato F Properties and origin of human Th17 cells Mol Immunol 2009;47:3-7 11 Ueno H, Banchereau J, Vinuesa CG Pathophysiology of T follicular helper cells in humans and mice Nat Immunol 2015;16:142-152 12 Pan HF, Leng RX, Li XP, Guo Zheng S, Ye DQ Targeting T-helper cells and interleukin-9 in autoimmune diseases Cytokine Growth Factor Rev 2013;24:515-522 13 Kaplan MH, Hufford MM, Olson MR The development and in vivo function of T helper cells Nat Rev Immunol 2015;15:295307 14 Hein F, Massin F, Cravoisy-Popovic A, et al The relationship between CD4+CD25+CD1272regulatory T cells and inflammatory response and outcome during shock states Crit Care 2010;14:R19 15 Muszynski JA, Nofziger R, Greathouse K, et al Early adaptive immune suppression in children with septic shock: a prospective observational study Crit Care 2014;18:R145 16 Venet F, Chung CS, Kherouf H, et al Increased circulating regulatory T cells (CD4(1)CD25 (1)CD127 (-)) contribute to lymphocyte anergy in septic shock patients Intensive Care Med 2009; 35:678-686 17 Venet F, Pachot A, Debard AL, et al Increased percentage of CD41CD251 regulatory T cells during septic shock is due to the decrease of CD41CD25- lymphocytes Crit Care Med 2004;32: 2329-2331 18 Wu HP, Chung K, Lin CY, Jiang BY, Chuang DY, Liu YC Associations of T helper 1, 2, 17 and regulatory T lymphocytes with mortality in severe sepsis Inflamm Res 2013;62:751-763 19 Fahl SP, Coffey F, Wiest DL Origins of gammadelta T cell effector subsets: a riddle wrapped in an enigma J Immunol 2014;193:42894294 20 Robertson FC, Berzofsky JA, Terabe M NKT cell networks in the regulation of tumor immunity Front Immunol 2014;5:543 21 Allen ML, Hoschtitzky JA, Peters MJ, et al Interleukin-10 and its role in clinical immunoparalysis following pediatric cardiac surgery Crit Care Med 2006;34:2658-2665 22 Hall MW, Geyer SM, Guo CY, et al Innate immune function and mortality in critically ill children with influenza: a multicenter study Crit Care Med 2013;41:224-236 23 Hall MW, Knatz NL, Vetterly C, et al Immunoparalysis and nosocomial infection in children with multiple organ dysfunction syndrome Intensive Care Med 2011;37:525-532 24 Muszynski JA, Nofziger R, Greathouse K, et al Innate immune function predicts the development of nosocomial infection in critically injured children Shock 2014;42:313-321 25 Muszynski JA, Nofziger R, Moore-Clingenpeel M, et al Early immune function and duration of organ dysfunction in critically ill children with sepsis Am J Respir Crit Care Med 2018;198:361-369 26 Wong HR, Cvijanovich N, Lin R, et al Identification of pediatric septic shock subclasses based on genome-wide expression profiling BMC Med 2009;7:34 27 Wong HR, Cvijanovich NZ, Allen GL, et al Corticosteroids are associated with repression of adaptive immunity gene programs in pediatric septic shock Am J Respir Crit Care Med 2014;189:940946 28 Wong HR, Freishtat RJ, Monaco M, et al Leukocyte subset-derived genomewide expression profiles in pediatric septic shock Pediatr Crit Care Med 2010;11:349-355 29 Felmet KA, Hall MW, Clark RS, Jaffe R, Carcillo JA Prolonged lymphopenia, lymphoid depletion, and hypoprolactinemia in children with nosocomial sepsis and multiple organ failure J Immunol 2005;174:3765-3772 30 Hotchkiss RS, Tinsley KW, Swanson PE, et al Sepsis-induced apoptosis causes progressive profound depletion of B and CD41 T lymphocytes in humans J Immunol 2001;166:6952-6963 31 Chang KC, Burnham CA, Compton SM, et al Blockade of the negative co-stimulatory molecules PD-1 and CTLA-4 improves survival in primary and secondary fungal sepsis Crit Care 2013; 17:R85 32 Inoue S, Bo L, Bian J, Unsinger J, Chang K, Hotchkiss RS Dosedependent effect of anti-CTLA-4 on survival in sepsis Shock 2011; 36:38-44 33 Reinke P, Volk HD Diagnostic and predictive value of an immune monitoring program for complications after kidney transplantation Urol Int 1992;49:69-75 34 Maude SL, Barrett D, Teachey DT, Grupp SA Managing cytokine release syndrome associated with novel T cell-engaging therapies Cancer J 2014;20:119-122 35 Yu AL, Gilman AL, Ozkaynak MF, et al Anti-GD2 antibody with GM-CSF, interleukin-2, and isotretinoin for neuroblastoma N Engl J Med 2010;363:1324-1334 36 Capitini CM, Otto M, DeSantes KB, Sondel PM Immunotherapy in pediatric malignancies: current status and future perspectives Future Oncol 2014;10:1659-1678 37 Grupp SA, Kalos M, Barrett D, et al Chimeric antigen receptormodified T cells for acute lymphoid leukemia N Engl J Med 2013;368:1509-1518 38 Maude SL, Laetsch TW, Buechner J, et al Tisagenlecleucel in children and young adults with B-cell lymphphoblasitic leukemia N Engl J Med 2018;378:439-448 e2 Abstract: A well-coordinated and functioning immune response is vital to maintaining health and to recovering from critical illness As such, it is important for the pediatric intensivist to understand elements of both the innate and adaptive immune systems This chapter reviews development and function of the cellular elements of adaptive immunity, adaptive immune activation, crosstalk between innate and adaptive immune responses, and clinical topics that are related to adaptive immunity and are of particular relevance to pediatric critical care medicine Key words: T lymphocyte, B lymphocyte, antibody, humoral immunity, cell-mediated immunity 102 Critical Illness and the Microbiome RAFAEL G RAMOS-JIMENEZ, DENNIS SIMON, AND MICHAEL J MOROWITZ • The term microbiome was first used to describe the collective genome of a microbial ecosystem in 2001.1,2 By 2007, the National Institutes of Health (NIH) had launched the first phase of the Human Microbiome Project (HMP) with the objective of describing the bacterial communities of healthy individuals.1,3 Although these initial studies showed substantial interindividual variation at lower phylogenetic levels, such as genus and species, the phyla Bacteroidetes and Firmicutes clearly emerged as dominant in the healthy gut, and Actinobacteria and Firmicutes were shown to be the dominant skin phyla.4 The clear dominance of a limited set of phyla (and the absence of most others) colonizing human body niches highlights the long nonrandom coevolution between humans and bacteria.5 Interestingly, the wide taxonomic variation seen in the gut microbiome of healthy individuals disappears at the gene level Even during the unstable period of infancy, gut microbes maintain a relatively constant abundance of genes that encode for specific metabolic pathways.6–9 This genetic “core” can be attained by different combinations of taxa, which explains why different taxonomic configurations are all compatible with health and the consistent association between taxonomic diversity and a healthy microbiome.10 The important insight provided by genomic studies was that the functional diversity that allows gut microbes to adapt to environmental, physiologic, and nutritional changes is found at the genomic level, not the taxonomic level The collective genome of the community, known as a metagenome, is what maintains ecologic stability and appropriate nutrient cycling.11,12 At present, the study of microbiome science is moving from correlation to causation.13–18 The current approach to microbiome research integrates taxonomic, genomic, proteomic, physiologic, and metabolic data to allow contextualization of microbial communities, mechanistic descriptions, and biomarker identification In 2014, the second phase of the HMP, known as the integrative HMP (iHMP), was launched by the NIH with the goal of describing the microbiome in pregnancy, inflammatory bowel 1208 • Like all organisms, humans have evolved in concert with microbes that serve numerous physiologic and immune functions during normal development and homeostasis Critical illness in both children and adults has been associated with profound changes in the microbiome at numerous body sites • • PEARLS The short- and long-term clinical consequences of these changes in the microbiome have not been clearly elucidated Despite huge leaps in our understanding of host microbiome interactions during health and disease, the human microbiome’s diagnostic, prognostic, and therapeutic potential is yet to be realized disease (IBD), and type diabetes—three important conditions linked previously to aberrant patterns of microbial colonization The initial results of the iHMP have already refined and expanded our understanding of host-microbe relationships in health and disease, moving microbiome science further from correlation and closer to causation.3 General Concepts in the Field of Microbiome Science Commensal, Pathogenic, and Keystone Species The term commensal describes an ecologic relation between two organisms in which the commensal benefits and the host is neither benefited nor harmed.19 Our understanding of the human microbiome suggests that bacteria have a mutualistic relationship with us rather than a commensal one That is, both the bacteria and their human host benefit from the relationship On the other hand, pathogenic species are those that, when present in a host, can cause disease However, many studies show that these distinctions are fluid in the context of the human microbiome, where nutrient availability, presence of pathogenicity islands, and inflammation can turn mutualists into pathogens.12,20–22 Another important concept is that of keystone species, which are “highly connected taxa that individually or in a guild exert a considerable influence on microbiome structure and functioning irrespective of their abundance across space and time.”23 Site Specificity The human body provides microorganisms with hugely divergent ecosystems to colonize These ecosystems range from the anaerobic and nutrient-rich gut lumen to the aerobic but nutrientdepleted stratified squamous epithelia of the skin The different habitats select for different microbes leading to site specificity, CHAPTER 102 Critical Illness and the Microbiome which is the well-described observation that microbial community membership varies predictably depending on the sampled body location.3,4,24 Although not yet proven, it has been postulated that loss of site specificity may portend worse outcomes in both critically ill children and adults.22,25 Dysbiosis The term dysbiosis has been loosely applied in the literature to any deviation from a healthy microbiome, especially when this deviation is associated with disease.22,26,27 These shifts have been associated with changes in diet, disease states, antibiotic use, surgical trauma, and many other insults.20 In the context of critical illness, a useful definition of dysbiosis is “a state of microbial organ dysfunction, a condition in which the gut-associated microbial community becomes a liability because the host no longer maintains proper control over the ecosystem.”28,29 This dysfunction is most consistently associated with a shift from obligate to facultative anaerobes in the gut.28 Although many ecologic perturbations are transient, the dysbiotic state persists when an insult is chronic, such as in IBD, or severe enough in acute conditions to cause a loss of keystone species.30–33 This persistent dysbiosis is further exacerbated by physiologic insults accompanying acute critical illness that increase expression of virulence factors even among commensal organisms.11,12 The persistence of these dysfunctional communities has been associated with immunologic dysfunction, increased inflammation, and increased epithelial permeability, suggesting a role for the microbiome as both a cause and/or a consequence of critical illness (Fig 102.1).33–36 As discussed later, it is not yet known whether intensive care unit (ICU)–related dysbiosis resolves over Healthy 1209 time in patients who experience clinical improvement and whether microbiome-targeted therapies to reverse dysbiosis can hasten patient recovery or improve outcomes This chapter focuses on the bacterial component of the human microbiome However, it is important to note that the human microbiome also consists of viral, fungal, and protozoan communities that are currently harder to study for technical reasons.37,38 For example, study of the human virome, which includes viruses that infect human cells as well as other microbes within the body (e.g., bacteriophages), is limited because (1) viruses not contain a conserved genomic region, such as the 16S gene in bacteria; and (2) many viruses are not included in viral databases.39 Newer techniques (see later discussion on metagenomic sequencing), although more expensive than amplicon sequencing, have overcome several barriers to studying nonbacterial communities in the human microbiome and revealed increasingly complex interactions within the microbiome and with the host in healthy and diseased states Studying the Microbiome Historically, clinical microbiology has relied heavily on the ability to cultivate pathogens from patient samples sent to clinical microbiology laboratories This approach works well for a sample such as cerebrospinal fluid, which should be sterile but in some circumstances may contain a heavy burden of a single causative pathogen However, this approach is less effective in characterizing mixed communities of organisms—especially in samples such as stool or sputum, with high bacterial density even in the absence of infection One reason for this problem is that many or most organisms within the human microbiome cannot be cultivated for Critically ill Lung microbiota dysbiosis Effective elimination of pathogens Difficulty to eliminate pathogens Immunomodulation Dysregulated immunomodulation Priming of immune system through bacterial ligands and metabolites Intestinal microbiota dysbiosis due to critical illness and given therapies, such as antibiotics Intestinal bacteria give protection against local invasion of pathogens Intestine loses protection against local invasion of pathogens • Fig 102.1 The gut and lung microbiota in critical illness Healthy microbial communities in the human gut and lung protect against colonization by pathogens In critically ill patients with dysbiotic microbial communities, these protective responses are compromised (From Wolff NS, Hugenholtz F, Wiersing WJ The emerging role of the microbiota in the ICU Crit Care 2018;22.) 1210 S E C T I O N X I Pediatric Critical Care: Immunity and Infection TABLE 102.1 Schematic Overview of a Compartmentalized Host-Microbe Metabolic Model Setup Data Type (Meta)genomics Meta(proteomics), Meta(transcriptomics) Input data 16S rRNA data Metagenomic reads Host genetics Affected constraints Microbiome composition and relative abundances Host phenotype Metabolomics Nutrition Gene expression levels Protein levels Media metabolites Stool metabolites Blood metabolites Urine metabolites Food frequency questionnaires Standardized diets Growth media Active metabolic pathways in individual microbes and host reconstruction Output metabolites Metabolite secretion into body fluids Input metabolites technical reasons.40 This may change with time with new knowledge about the metabolic and nutritional requirements of humanassociated microbes It is important for clinicians and scientists alike to realize that culture-dependent and culture-independent studies of the microbiota each have advantages and disadvantages The ability to complement or bypass laboratory culture in the study of the human microbiome has improved dramatically as a result of three recent scientific advances: high-throughput nucleic acid sequencing, the use of gene sequences encoding the 16S ribosomal subunit to enable taxonomic assignments, and the development of robust bioinformatic methods to analyze and interpret these results Similar to -omics studies of the human genome, culture-independent studies of the microbiome can be categorized into several categories depending on the input variables of the experiment (Table 102.1), for example, DNA or RNA Bacterial profiling of microbiome samples is commonly based on analysis of a 1.5-Kbp gene that encodes the subunit of bacterial ribosomes The nine hypervariable regions (V1–V9) of this gene are highly conserved among bacterial phyla but variable at lower taxonomic levels, making it an effective phylogenetic marker.42,43 16S rRNA gene sequencing results typically contain genes from numerous organisms, which can be identified using reference databases such as the Ribosomal Database Project (myRDP) or Silva This process is called closed reference operational taxonomic unit picking.44,45 In the case of the human gut microbiome, for example, extensive reference databases exist that are reliable and provide good specificity and sensitivity.14 In samples without extensive reference databases, such as respiratory samples, more challenging bioinformatic methods may be required to identify the bacterial composition present within the samples.46,47 Once taxonomic assignments have been made, diversity measures can be calculated The most commonly used diversity measures are alpha diversity and beta diversity Alpha diversity measures the number of taxa within an environment, while beta diversity quantifies differences between environments In other words, alpha diversity describes a single population, while beta diversity describes two or more populations.47–49 In summary, the steps of a typical taxonomic analysis are extraction of DNA from a sample (stool, saliva, etc.), targeted or untargeted (see later discussion) sequencing of microbial DNA, taxonomy assignment, and community analyses of diversity Whole-genome sequencing, or metagenomics, is another commonly used technique to study the microbiome but is more costly and labor intensive This technique consists of sequencing and characterizing all of the microbial DNA present within a sample Whereas 16S rRNA gene sequences are effective in profiling community membership, metagenomic sequencing studies are unbiased analyses of all genetic information present within microbial communities In theory, metagenomic studies are not restricted to bacteria and offer the potential not only to identify which organisms are present but also to catalog all genes present, to predict their metabolic or virulence potential, and, in some cases, assemble entire microbial genomes.50,51 Complementary -omics studies build on studies of DNA content to characterize the RNA, protein, and/or metabolites present within a given sample Development of the Microbiome in Children Prior to delivery, the fetus is considered to be sterile or near-sterile.52 Cesarean and vaginal delivery each expose the newborn to a significant burden of bacteria; predominantly skin and oral flora in the case of cesarean delivery and vaginal and intestinal flora such as Enterobacteriaceae and Bacteroidaceae in the case of vaginal delivery Controversy exists as to whether the mode of delivery confers lasting changes in bacterial colonization However, no functional differences of the microbiome have been observed between infants born by vaginal or cesarean delivery Recent evidence describing amniotic, placental, and meconium microbiomes suggests that maternal-fetal microbiota transfer may also occur.53 Site specificity of the microbiome has been observed at as early as weeks of life.54 At this age, stool, oral, and skin microbiota cluster distinctly and are enriched with characteristic microbiota— for example, Streptococcus in oral samples, Staphylococcus and Corynebacterium in skin samples, and Bacteroides in stool samples Diet significantly influences the development of the infant microbiome Multiple studies have demonstrated differences in gut microbiota between breastfed and formula-fed infants.55 Breastfed infants receive significant bacterial exposure from breastmilk, which contains high quantities of Lactobacillus and Bifidobacterium spp These bacteria are able to synthesize compounds with antimicrobial effects against pathogenic bacteria and which assist digestion of human milk Formula-fed infants have a higher prevalence of Clostridium and Roseburia spp in their gut and overall have reduced alpha- and beta-diversity relative to breastfed children.56 Following the introduction of cereals and other solid foods, a rapid expansion of diversity occurs in the infant gut with an increase in relative abundance of obligate anaerobic bacteria, including Bacteroidetes and Firmicutes By approximately to years of age, the microbiome of children resembles that of adults and ... laboratories This approach works well for a sample such as cerebrospinal fluid, which should be sterile but in some circumstances may contain a heavy burden of a single causative pathogen However, this... with high bacterial density even in the absence of infection One reason for this problem is that many or most organisms within the human microbiome cannot be cultivated for Critically ill Lung microbiota... microbiome but is more costly and labor intensive This technique consists of sequencing and characterizing all of the microbial DNA present within a sample Whereas 16S rRNA gene sequences are