Antibiotic use in children is associated with increased risk of asthma

Association of Previous Antibiotics Use and Kawasaki Disease: A Cohort Study of 106,908 Patients

BACKGROUND

Microbial imbalance in the gut from antibiotic use may be an etiologic factor of Kawasaki disease (KD). We aimed to identify the association between the use of antibiotics and the development of KD, considering various antibiotic profiles.

METHODS

A population-based, case-control study was performed using data from the Health Insurance Review and Assessment Service database. Children <5 years of age, who were diagnosed with KD between 2016 and 2019, were identified. Propensity score-matched controls were selected from the general population in a 1:5 ratio. Four separate study cohorts were created according to different periods of antibiotic use: (1) within 28 days and (2) 12 months after birth and (3) within 6 months and (4) 12 months from the index date. Profiles regarding antibiotic use were compared between patients with KD and matched controls.

RESULTS

We included 17,818 patients with KD and 89,090 matched controls. Use of antibiotics within 6 months [odds ratio (OR): 1.18; 95% confidence interval (CI): 1.12-1.26] and 12 months (OR: 1.23; 95% CI: 1.14-1.32) from the index date were associated with the development of KD. The association between antibiotic use and KD was most prominent in patients who had received 3 or more types of antibiotics within 12 months from the index date (OR: 1.26; 95% CI: 1.17-1.37).

CONCLUSIONS

Antibiotic use within the preceding 6 or 12 months was associated with KD. Alteration in gut microbiota due to antibiotic usage might play a role in the development of KD.

Antibiotic treatment to prevent pediatric acute otitis media infectious complications: A meta-analysis

BACKGROUND

Most US children with acute otitis media [AOM] receive prompt antibiotic treatment, though guidelines encourage watchful waiting. Previous systematic reviews of antibiotics versus watchful waiting have focused on symptom resolution and RCTs, limiting the assessment of serious, rare complications. We sought to evaluate these complications by including observational studies.

METHODS

RCTs and observational studies that compared antibiotics to placebo or watchful waiting for pediatric clinician diagnosed AOM were identified [PubMed/MEDLINE, Embase, Cochrane Database of Systematic Reviews, Central Register of Controlled Trials, and Web of Science] and reviewed for meta-analysis. Two reviewers independently extracted study characteristics, patient characteristics, and outcomes. We assessed publication bias, study bias with ROBINS-1 and RoB-2 and used random-effects models to assess treatment effects.

RESULTS

24 studies were included. Antibiotics decreased the risk of acute mastoiditis [incidence 0.02%, RR 0.48, 95% CI 0.40-0.59; NNT 5,368]. This protective effect may be underestimated because of misclassification of non-suppurative conditions as AOM. Intracranial complications remained too rare to assess. Antibiotics markedly increased the risk of adverse effects [incidence 10.5%, RR 1.49, 1.27-1.73; NNH 23]. Studies used non-specific criteria for acute mastoiditis, potentially underestimating treatment effects.

CONCLUSIONS

Prompt antibiotic therapy reduces the risk for some AOM complications. The NNT to prevent serious, rare complications is high, while the NNH is relatively low. Large-scale population-based observational studies using real-world datasets with validated measures of severe complications are needed to improve understanding of risk factors for serious AOM complications, facilitate more selective antibiotic therapy, and optimize individual outcomes and public health.

Understanding the influence of the microbiome on childhood infections

INTRODUCTION

The microbiome is known to have a substantial impact on human health and disease. However, the impacts of the microbiome on immune system development, susceptibility to infectious diseases, and vaccine-elicited immune responses are emerging areas of interest.

AREAS COVERED

In this review, we provide an overview of development of the microbiome during childhood. We highlight available data suggesting that the microbiome is critical to maturation of the immune system and modifies susceptibility to a variety of infections during childhood and adolescence, including respiratory tract infections, Clostridioides difficile infection, and sexually transmitted infections. We discuss currently available and investigational therapeutics that have the potential to modify the microbiome to prevent or treat infections among children. Finally, we review the accumulating evidence that the gut microbiome influences vaccine-elicited immune responses among children.

EXPERT OPINION

Recent advances in sequencing technologies have led to an explosion of studies associating the human microbiome with the risk and severity of infectious diseases. As our knowledge of the extent to which the microbiome influences childhood infections continues to grow, microbiome-based diagnostics and therapeutics will increasingly be incorporated into clinical practice to improve the prevention, diagnosis, and treatment of infectious diseases among children.

A Lipopolysaccharide-Enriched Cow's Milk Allergy Microbiome Promotes a TLR4-Dependent Proinflammatory Intestinal Immune Response

We have previously reported that the gut microbiota of healthy infants harbors allergy-protective bacteria taxa that are depleted in infants with cow's milk allergy (CMA). Few reports have investigated the role of the gut microbiota in promoting allergic responses. In this study we selected a CMA-associated microbiota with increased abundance of Gram-negative bacteria for analysis of its proinflammatory potential. LPS is the major component of the outer membrane of Gram-negative bacteria. Colonization of mice with a global or conditional mutation of the LPS receptor TLR4 with this CMA microbiota induced expression of serum amyloid A1 (Saa1) and other Th17-, B cell-, and Th2-associated genes in the ileal epithelium in a TLR4-dependent manner. In agreement with the gene expression data, mice colonized with the CMA microbiota have expanded populations of Th17 and regulatory T cells and elevated concentrations of fecal IgA. Importantly, we used both antibiotic-treated specific pathogen-free and germ-free rederived mice with a conditional mutation of TLR4 in the CD11c+ compartment to demonstrate that the induction of proinflammatory genes, fecal IgA, and Th17 cells is dependent on TLR4 signaling. Furthermore, metagenomic sequencing revealed that the CMA microbiota has an increased abundance of LPS biosynthesis genes. Taken together, our results show that a microbiota displaying a higher abundance of LPS genes is associated with TLR4-dependent proinflammatory gene expression and a mixed type 2/type 3 response in mice, which may be characteristic of a subset of infants with CMA.

A toxic environment selects for specialist microbiome in poison frogs

Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.

Predictors of recurrent wheezing in late preterm infants

INTRODUCTION

Premature infants have an increased risk of respiratory morbidity, including the development of recurrent wheezing. We sought to determine perinatal factors in late preterm infants associated with an increased risk of recurrent wheezing in the first 3 years of life.

METHODS

A retrospective chart review of infants born between 32 and 36 weeks gestational age at a tertiary hospital from 2013 to 2016 was performed. Infants with any co-morbid medical conditions were excluded. Recurrent wheezing was identified by two or more visit diagnoses for reactive airway disease, wheezing-associated respiratory infection, wheezing, or asthma during the first 3 years of life. Those with recurrent wheezing were compared to matched preterm infants who did not develop wheezing.

RESULTS

Three hundred and fourteen late preterm infants were included in this study; 210 infants developed recurrent wheezing while 104 did not. Gender, sex, and race were comparable between both groups. Development of wheezing was associated with positive family history of asthma (p = .014), receiving antibiotics during the neonatal period (p < .001), requiring continuous positive airway pressure for <24 h (p = .019), and receiving supplemental oxygen during the newborn period (p = .023).

CONCLUSION

This study retrospectively identified risk factors associated with development of wheezing in late preterm infants. Prospective studies are needed to determine whether these factors will predict recurrent wheeze in this patient population.

Winds of change a tale of: asthma and microbiome

The role of the microbiome in asthma is highlighted, considering its influence on immune responses and its connection to alterations in asthmatic patients. In this context, we review the variables influencing asthma phenotypes from a microbiome perspective and provide insights into the microbiome's role in asthma pathogenesis. Previous cohort studies in patients with asthma have shown that the presence of genera such as Bifidobacterium, Lactobacillus, Faecalibacterium, and Bacteroides in the gut microbiome has been associated with protection against the disease. While, the presence of other genera such as Haemophilus, Streptococcus, Staphylococcus, and Moraxella in the respiratory microbiome has been implicated in asthma pathogenesis, indicating a potential link between microbial dysbiosis and the development of asthma. Furthermore, respiratory infections have been demonstrated to impact the composition of the upper respiratory tract microbiota, increasing susceptibility to bacterial diseases and potentially triggering asthma exacerbations. By understanding the interplay between the microbiome and asthma, valuable insights into disease mechanisms can be gained, potentially leading to the development of novel therapeutic approaches.

The potential immunomodulatory role of the gut microbiota in the pathogenesis of asthma: an in vitro study

The aim of this study was to investigate the influence of Bacteroides vulgatus (BV), Clostridium perfringens (CP), Parabacteroides distasonis (PD) and Ruminococcus albus (RA) lysates on secretion of selected cytokines by PBMC, MDM and HT-29 cells, as well as to determine the potential mechanisms of their action in the development of asthma. Enzyme-linked immunosorbent assays were used to analyze the effect of BV, CP, PD and RA lysates on the secretion of IL-1β, IL-6, IL-10 and TNF-α by human PBMC, MDM and HT-29 cells. BV and CP lysates significantly lowered IL-1β secretion by MDM vs. control (p < 0.05 and p < 0.001 respectively) but only at a dose of 400 µg lysate. The secretions of IL-6 by PBMC and MDM were elevated significantly above control values (p < 0.05) after administration of CP and PD lysates. BV, CP and PD lysates (100 µg) significantly increased IL-10 secretion by PBMC vs. control (p < 0.05). CP, PD and RA lysates (400 µg) significantly increased IL-10 secretion by MDM vs. control (p < 0.001). BV lysate (400 µg) also significantly increased IL-10 secretion by MDM as compared to control (p < 0.05). In PBMC and MDM, the production levels of the anti-inflammatory cytokine were increased by all the bacterial lysates used in a dose-dependent manner.

Early-life interactions between the microbiota and immune system: impact on immune system development and atopic disease

Prenatal and early postnatal life represent key periods of immune system development. In addition to genetics and host biology, environment has a large and irreversible role in the immune maturation and health of an infant. One key player in this process is the gut microbiota, a diverse community of microorganisms that colonizes the human intestine. The diet, environment and medical interventions experienced by an infant determine the establishment and progression of the intestinal microbiota, which interacts with and trains the developing immune system. Several chronic immune-mediated diseases have been linked to an altered gut microbiota during early infancy. The recent rise in allergic disease incidence has been explained by the 'hygiene hypothesis', which states that societal changes in developed countries have led to reduced early-life microbial exposures, negatively impacting immunity. Although human cohort studies across the globe have established a correlation between early-life microbiota composition and atopy, mechanistic links and specific host-microorganism interactions are still being uncovered. Here, we detail the progression of immune system and microbiota maturation in early life, highlight the mechanistic links between microbes and the immune system, and summarize the role of early-life host-microorganism interactions in allergic disease development.

Early-immune development in asthma: A review of the literature

This review presents a comprehensive examination of the various factors contributing to the immunopathogenesis of asthma from the prenatal to preschool period. We focus on the contributions of genetic and environmental components as well as the role of the nasal and gut microbiome on immune development. Predisposing genetic factors, including inherited genes associated with increased susceptibility to asthma, are discussed alongside environmental factors such as respiratory viruses and pollutant exposure, which can trigger or exacerbate asthma symptoms. Furthermore, the intricate interplay between the nasal and gut microbiome and the immune system is explored, emphasizing their influence on allergic immune development and response to environmental stimuli. This body of literature underscores the necessity of a comprehensive approach to comprehend and manage asthma, as it emphasizes the interactions of multiple factors in immune development and disease progression.

Antibiotic use and development of nonalcoholic fatty liver disease: A population-based case-control study

BACKGROUND AND AIMS

Antibiotics affect the gut microbiome. Preclinical studies suggest a role of gut dysbiosis in the development of nonalcoholic fatty liver disease (NAFLD), but data from large cohorts with liver histology are lacking.

METHODS

In this nationwide case-control study, Swedish adults with histologically confirmed early-stage NAFLD (total n = 2584; simple steatosis n = 1435; steatohepatitis (NASH) n = 383; non-cirrhotic fibrosis n = 766) diagnosed January 2007-April 2017 were included and matched to ≤5 population controls (n = 12 646) for age, sex, calendar year and county of residence. Data for cumulative antibiotic dispensations and defined daily doses were accrued until 1 year before the matching date. Using conditional logistic regression, multivariable-adjusted odds ratios (aORs) were calculated. In a secondary analysis, NAFLD patients were compared with their full siblings (n = 2837).

RESULTS

Previous antibiotic use was seen in 1748 (68%) NAFLD patients versus 7001 (55%) controls, corresponding to 1.35-fold increased odds of NAFLD (95% CI = 1.21-1.51) in a dose-dependent manner (pfor trend  < .001). Estimates were comparable for all histologic stages (p > .05). The highest risk of NAFLD was observed after treatment with fluoroquinolones (aOR 1.38; 95% CI = 1.17-1.59). Associations remained robust when patients were compared with their full siblings (aOR 1.29; 95% CI = 1.08-1.55). Antibiotic treatment was only linked to NAFLD in patients without metabolic syndrome (aOR 1.63; 95% CI = 1.35-1.91) but not in those with metabolic syndrome (aOR 1.09; 95% CI = 0.88-1.30).

CONCLUSIONS

Antibiotic use may be a risk factor for incident NAFLD, especially in individuals without the metabolic syndrome. The risk was highest for fluoroquinolones and remained robust in sibling comparisons with whom individuals share genetic and early environmental susceptibilities.

Managing the clinical effects of drug-induced intestinal dysbiosis with a focus to antibiotics: Challenges and opportunities

The term "intestinal dysbiosis" is used for indicating change(s) of the intestinal microbiota which have been associated with the development of diseases and the deterioration of disease treatments in humans. In this review, documented clinical effects of drug-induced intestinal dysbiosis are briefly presented, and methodologies which could be considered for the management of drug-induced intestinal dysbiosis based on clinical data are critically reviewed. Until relevant methodologies are optimized and/or their effectiveness to the general population is confirmed, and, since drug-induced intestinal dysbiosis refers predominantly to antibiotic-specific intestinal dysbiosis, a pharmacokinetically-based approach for mitigating the impact of antimicrobial therapy on intestinal dysbiosis is proposed.

Prenatal, Intrapartum, and Neonatal Factors Increase the Risk of Eosinophilic Esophagitis

INTRODUCTION

Early-life exposures have been associated with an increased risk of eosinophilic esophagitis (EoE); however, most studies to date have been conducted at referral centers and are subject to recall bias. By contrast, we conducted a nationwide, population-based and registry-based case-control study of prenatal, intrapartum, and neonatal exposures, using data collected prospectively through population-based Danish health and administrative registries.

METHODS

We ascertained all EoE cases in Denmark (birth years 1997-2018). Cases were sex and age matched to controls (1:10) using risk-set sampling. We obtained data on prenatal, intrapartum, and neonatal factors, i.e., pregnancy complications, mode of delivery, gestational age at delivery, birthweight (expressed as a z-score), and neonatal intensive care unit (NICU) admission. We used conditional logistic regression to compute the crude and adjusted odds ratios (aOR) of EoE in relation to each prenatal, intrapartum, and neonatal factor, thus providing an estimate of incidence density ratios with 95% confidence intervals (CI).

RESULTS

In the 393 cases and 3,659 population controls included (median age at index date, 11 years [interquartile range, 6-15]; 69% male), we observed an association between gestational age and EoE, peaking at 33 vs 40 weeks (aOR 3.6 [95% CI 1.8-7.4]), and between NICU admission and EoE (aOR 2.8 [95% CI 1.2-6.6], for a NICU hospitalization of 2-3 weeks vs no admission). In interaction analyses, we observed a stronger association between NICU admission and EoE in infants born at term than in preterm infants (aOR 2.0 [95% CI 1.4-2.9] for term infants and aOR 1.0 [95% CI 0.5-2.0] for preterm infants). We also observed an association between pregnancy complications and EoE (aOR 1.4 [95% CI 1.0-1.9]). Infants who were very growth restricted at birth had an increased rate of EoE (aOR 1.4 [95% CI: 1.0-1.9] for a z-score of -1.5 vs a z-score of 0). Mode of delivery was not associated with EoE.

DISCUSSION

Prenatal, intrapartum, and neonatal factors, particularly preterm birth and NICU admission, were associated with development of EoE. Further research is needed to elucidate the mechanisms underlying the observed associations.

Interferons as negative regulators of ILC2s in allergic lung inflammation and respiratory viral infections

Group 2 innate lymphoid cells (ILC2s), characterized by a lack of antigen receptors, have been regarded as an important component of type 2 pulmonary immunity. Analogous to Th2 cells, ILC2s are capable of releasing type 2 cytokines and amphiregulin, thus playing an essential role in a variety of diseases, such as allergic diseases and virus-induced respiratory diseases. Interferons (IFNs), an important family of cytokines with potent antiviral effects, can be triggered by microbial products, microbial exposure, and pathogen infections. Interestingly, the past few years have witnessed encouraging progress in revealing the important role of IFNs and IFN-producing cells in modulating ILC2 responses in allergic lung inflammation and respiratory viral infections. This review underscores recent progress in understanding the role of IFNs and IFN-producing cells in shaping ILC2 responses and discusses disease phenotypes, mechanisms, and therapeutic targets in the context of allergic lung inflammation and infections with viruses, including influenza virus, rhinovirus (RV), respiratory syncytial virus (RSV), and severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2).

Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review

BACKGROUND

Inappropriate antimicrobial usage is a key driver of antimicrobial resistance (AMR). Low- and middle-income countries (LMICs) are disproportionately burdened by AMR and young children are especially vulnerable to infections with AMR-bearing pathogens. The impact of antibiotics on the microbiome, selection, persistence, and horizontal spread of AMR genes is insufficiently characterized and understood in children in LMICs. This systematic review aims to collate and evaluate the available literature describing the impact of antibiotics on the infant gut microbiome and resistome in LMICs.

METHODS AND FINDINGS

In this systematic review, we searched the online databases MEDLINE (1946 to 28 January 2023), EMBASE (1947 to 28 January 2023), SCOPUS (1945 to 29 January 2023), WHO Global Index Medicus (searched up to 29 January 2023), and SciELO (searched up to 29 January 2023). A total of 4,369 articles were retrieved across the databases. Duplicates were removed resulting in 2,748 unique articles. Screening by title and abstract excluded 2,666 articles, 92 articles were assessed based on the full text, and 10 studies met the eligibility criteria that included human studies conducted in LMICs among children below the age of 2 that reported gut microbiome composition and/or resistome composition (AMR genes) following antibiotic usage. The included studies were all randomized control trials (RCTs) and were assessed for risk of bias using the Cochrane risk-of-bias for randomized studies tool. Overall, antibiotics reduced gut microbiome diversity and increased antibiotic-specific resistance gene abundance in antibiotic treatment groups as compared to the placebo. The most widely tested antibiotic was azithromycin that decreased the diversity of the gut microbiome and significantly increased macrolide resistance as early as 5 days posttreatment. A major limitation of this study was paucity of available studies that cover this subject area. Specifically, the range of antibiotics assessed did not include the most commonly used antibiotics in LMIC populations.

CONCLUSION

In this study, we observed that antibiotics significantly reduce the diversity and alter the composition of the infant gut microbiome in LMICs, while concomitantly selecting for resistance genes whose persistence can last for months following treatment. Considerable heterogeneity in study methodology, timing and duration of sampling, and sequencing methodology in currently available research limit insights into antibiotic impacts on the microbiome and resistome in children in LMICs. More research is urgently needed to fill this gap in order to better understand whether antibiotic-driven reductions in microbiome diversity and selection of AMR genes place LMIC children at risk for adverse health outcomes, including infections with AMR-bearing pathogens.

Perturbation of maternal gut microbiota in mice during a critical perinatal window influences early neurobehavioral outcomes in offspring

The gut microbiota is increasingly recognized as a key environmental factor that shapes host development and physiology, including neural circuits formation and function. Concurrently, there has been growing concern that early-life antibiotic exposure may alter brain developmental trajectories, increasing the risk for neurodevelopmental disorders such as autism spectrum disorder (ASD). Here, we assessed whether perturbation of the maternal gut microbiota in mice during a narrow critical perinatal window (last week of pregnancy and first three postnatal days), induced by exposure to a commonly used broad-spectrum oral antibiotic (ampicillin), influences offspring neurobehavioral outcomes relevant to ASD. Our results demonstrate that neonatal offspring from antibiotic-treated dams display an altered pattern of ultrasonic communication, which was more pronounced in males. Moreover, juvenile male, but not female, offspring from antibiotic-treated dams showed reduced social motivation and social interaction, as well as context-dependent anxiety-like behavior. However, no changes were observed in locomotor or exploratory activity. This behavioral phenotype of exposed juvenile males was associated with reduced gene expression of the oxytocin receptor (OXTR) and several tight-junction proteins in the prefrontal cortex, a key region involved in the regulation of social and emotional behaviors, as well as a mild inflammatory response in the colon. Further, juvenile offspring from exposed dams also showed distinct alterations in several gut bacterial species, including, Lactobacillus murinus, and Parabacteroides goldsteinii. Overall, this study highlights the importance of the maternal microbiome in early-life, and how its perturbation by a widely used antibiotic could contribute to atypical social and emotional development of offspring in a sex-dependent manner.

Model-estimated impacts of pediatric respiratory syncytial virus prevention programs in Mali on asthma prevalence

Background

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infection (LRTI) in young children and is associated with subsequent recurrent wheezing illness and asthma (wheeze/asthma). RSV prevention may therefore reduce wheeze/asthma prevalence.

Objectives

We estimated the contribution of RSV LRTI and the impact of RSV prevention on recurrent wheeze/asthma in Mali.

Methods

We simulated 12 consecutive monthly birth cohorts in Mali and estimated RSV LRTI cases through 2 years and recurrent wheeze/asthma prevalence at 6 years under different RSV prevention scenarios: status quo, seasonal birth-dose extended half-life mAb, and seasonal birth-dose extended half-life mAb followed by 2 doses of pediatric vaccine (mAb + vaccine). We used World Health Organization (WHO) Preferred Product Characteristics for RSV prevention, demographic and RSV epidemiologic data from Mali, regional recurrent wheeze/asthma prevalence, and relative risk of recurrent wheeze/asthma given early childhood RSV LRTI.

Results

Among the simulated cohort of 778,680 live births, 10.0% had RSV LRTI by 2 years and 89.6% survived to 6 years. We estimated that 13.4% of all recurrent wheeze/asthma at 6 years was attributable to RSV LRTI. Recurrent wheeze/asthma prevalence at 6 years was 145.0 per 10,000 persons (RSV LRTI attributable) and 1084.2 per 10,000 persons (total). In mAb and mAb + vaccine scenarios, RSV LRTI cases decreased by 11.8% and 44.4%, respectively, and recurrent wheeze/asthma prevalence decreased by 11.8% and 44.4% (RSV LRTI attributable) and 1.6% and 5.9% (total).

Conclusion

In Mali, RSV prevention programs may have a meaningful impact on chronic respiratory disease, strengthening the case for investment in RSV prevention.

Human gut microbiome: A primer for the clinician

The human host gets tremendously influenced by a genetically and phenotypically distinct and heterogeneous constellation of microbial species-the human microbiome-the gut being one of the most densely populated and characterized site for these organisms. Microbiome science has advanced rapidly, technically with respect to the analytical methods and biologically with respect to its mechanistic influence in health and disease states. A clinician conducting a microbiome study should be aware of the nuances related to microbiome research, especially with respect to the technical and biological factors that can influence the interpretation of research outcomes. Hence, this review is an attempt to detail these aspects of the human gut microbiome, with emphasis on its determinants in a healthy state.

The importance of the timing of microbial signals for perinatal immune system development

Background: Development and maturation of the immune system begin in utero and continue throughout the neonatal period. Both the maternal and neonatal gut microbiome influence immune development, but the relative importance of the prenatal and postnatal periods is unclear. Methods: In the present study, we characterized immune cell populations in mice in which the timing of microbiome colonization was strictly controlled using gnotobiotic methodology. Results: Compared to conventional (CONV) mice, germ-free (GF) mice conventionalized at birth (EC mice) showed few differences in immune cell populations in adulthood, explaining only 2.36% of the variation in immune phenotypes. In contrast, delaying conventionalization to the fourth week of life (DC mice) affected seven splenic immune cell populations in adulthood, including dendritic cells and regulatory T cells (Tregs), explaining 29.01% of the variation in immune phenotypes. Early life treatment of DC mice with Limosilactobacillus reuteri restored splenic dendritic cells and Tregs to levels observed in EC mice, and there were strain-specific effects on splenic CD4+ T cells, CD8+ T cells, and CD11c+ F4/80+ mononuclear phagocytes. Conclusion: This work demonstrates that the early postnatal period, compared to the prenatal period, is relatively more important for microbial signals to influence immune development in mice. Our findings further show that targeted microbial treatments in early life can redress adverse effects on immune development caused by the delayed acquisition of the neonatal gut microbiome.

Investigating the effect of early life antibiotic use on asthma and allergy risk in over 600 000 Canadian children: a protocol for a retrospective cohort study in British Columbia and Manitoba

INTRODUCTION

Allergic conditions, such as asthma, hay fever and eczema, are some of the most common conditions impacting children globally. There is a strong incentive to study their determinants to improve their prevention. Asthma, hay fever and eczema are influenced through the same immunological pathway and often copresent in children ('the atopic march'). Increasing evidence shows a link between infant antibiotic use and the risk of childhood atopic conditions, mediated through gut microbial dysbiosis during immune system maturation, however, the potential for confounding remains. This study will investigate the relationship between infant antibiotic use and risk of allergic conditions in British Columbian and Manitoban children born over 10 years, adjusting for relevant confounders.

METHODS AND ANALYSIS

Provincial administrative datasets will be linked to perform comparable retrospective cohort analyses, using Population Data BC and the Manitoba Population Research Data Repository. All infants born between 2001 and 2011 in BC and Manitoba will be included (approximately 460 000 and 162 500 infants, respectively), following up to age 7. Multivariable logistic regression will determine the outcome risk by the fifth birthday among children who did and did not receive antibiotics before their first birthday. Clinical, demographic and environmental covariates will be explored, and sensitivity analyses performed to reduce confounding by indication.

ETHICS AND DISSEMINATION

The University of British Columbia Research Ethics Board (H19-03255) and University of Manitoba Ethics Board (HS25156 (H2021:328)) have approved this study. Data stewardship committees for all administrative datasets have granted permissions, facilitated by Population Data BC and the Manitoba Centre for Health Policy. Permissions from the Canadian Health Infant Longitudinal Development Study are being sought for breastfeeding data (CP185). Findings will be published in scientific journals and presented at infectious disease and respiratory health conferences. A stakeholder committee will guide and enhance sensitive and impactful communication of the findings to new parents.

Asthma occurrence in children and early life systemic antibiotic use: an incidence density study

BACKGROUND

Results of studies evaluating the relationship between asthma occurrence and early life antibiotic use have been conflicting. The aim of this study was to investigate the relationship between occurrence of asthma in children and systemic antibiotic use in the first year of life based on an incidence density study with careful consideration of the temporal aspects of the determinant-outcome relationship.

METHODS

We conducted an incidence density study nested in a data collection project with information on 1128 mother-child pairs. Systemic antibiotic use in the first year of life was defined as excessive (≥ 4 courses) vs. non-excessive (< 4 courses) use based on information from weekly diaries. Events (cases) were defined as the first parent-reported occurrence of asthma in a child between 1 and 10 years of age. Population time 'at risk' was probed by sampling population moments (controls). Missing data were imputed. Multiple logistic regression was used to assess the association between current first asthma occurrence (incidence density) and systemic antibiotic use in the first year of life, to evaluate effect modification and adjust for confounding.

RESULTS

Forty-seven first asthma events and 147 population moments were included. Excessive systemic antibiotic use in the first year of life showed more than twice the incidence density of asthma compared to non-excessive use (adjusted IDR [95% CI]: 2.18 [0.98, 4.87], p = 0.06). The association was more pronounced in children who have had lower respiratory tract infections (LRTIs) in the first year of life compared to children who had no LRTIs in the first year of life (adjusted IDR [95% CI]: 5.17 [1.19, 22.52] versus 1.49 [0.54, 4.14]).

CONCLUSIONS

Excessive use of systemic antibiotics in the first year of life may play a role in the genesis of asthma in children. This effect is modified by the occurrence of LRTIs in the first year of life, with a stronger association observed in children experiencing LRTIs in the first year of life.

Microbiome and Asthma: Microbial Dysbiosis and the Origins, Phenotypes, Persistence, and Severity of Asthma

The importance of the microbiome, and of the gut-lung axis in the origin and persistence of asthma, is an ongoing field of investigation. The process of microbial colonisation in the first three years of life is fundamental for health, with the first hundred days of life being critical. Different factors are associated with early microbial dysbiosis, such as caesarean delivery, artificial lactation and antibiotic therapy, among others. Longitudinal cohort studies on gut and airway microbiome in children have found an association between microbial dysbiosis and asthma at later ages of life. A low α-diversity and relative abundance of certain commensal gut bacterial genera in the first year of life are associated with the development of asthma. Gut microbial dysbiosis, with a lower abundance of Phylum Firmicutes, could be related with increased risk of asthma. Upper airway microbial dysbiosis, especially early colonisation by Moraxella spp., is associated with recurrent viral infections and the development of asthma. Moreover, the bacteria in the respiratory system produce metabolites that may modify the inception of asthma and is progression. The role of the lung microbiome in asthma development has yet to be fully elucidated. Nevertheless, the most consistent finding in studies on lung microbiome is the increased bacterial load and the predominance of proteobacteria, especially Haemophilus spp. and Moraxella catarrhalis. In this review we shall update the knowledge on the association between microbial dysbiosis and the origins of asthma, as well as its persistence, phenotypes, and severity.

Development of the gut microbiota during early life in premature and term infants

BACKGROUND

The gastrointestinal (GI) microbiota has been linked to health consequences throughout life, from early life illnesses (e.g. sepsis and necrotising enterocolitis) to lifelong chronic conditions such as obesity and inflammatory bowel disease. It has also been observed that events in early life can lead to shifts in the microbiota, with some of these changes having been documented to persist into adulthood. A particularly extreme example of a divergent early GI microbiota occurs in premature neonates, who display a very different GI community to term infants. Certain characteristic patterns have been associated with negative health outcomes during the neonatal period, and these patterns may prove to have continual damaging effects if not resolved.

RESULTS

In this study we compared a set of premature infants with a paired set of term infants (n = 37 pairs) at 6 weeks of age and at 2 years of age. In the samples taken at 6 weeks of age we found microbial communities differing in both diversity and specific bacterial groups between the two infant cohorts. We identified clinical factors associated with over-abundance of potentially pathogenic organisms (e.g. Enterobacteriaceae) and reduced abundances of some beneficial organisms (e.g. Bifidobacterium). We contrasted these findings with samples taken at 2 years of age, which indicated that despite a very different initial gut microbiota, the two infant groups converged to a similar, more adult-like state. We identified clinical factors, including both prematurity and delivery method, which remain associated with components of the gut microbiota. Both clinical factors and microbial characteristics are compared to the occurrence of childhood wheeze and eczema, revealing associations between components of the GI microbiota and the development of these allergic conditions.

CONCLUSIONS

The faecal microbiota differs greatly between infants born at term and those born prematurely during early life, yet it converges over time. Despite this, early clinical factors remain significantly associated with the abundance of some bacterial groups at 2 years of age. Given the associations made between health conditions and the microbiota, factors that alter the makeup of the gut microbiota, and potentially its trajectory through life, could have important lifelong consequences.

Human matters in asthma: Considering the microbiome in pulmonary health

Microbial communities form an important symbiotic ecosystem within humans and have direct effects on health and well-being. Numerous exogenous factors including airborne triggers, diet, and drugs impact these established, but fragile communities across the human lifespan. Crosstalk between the mucosal microbiota and the immune system as well as the gut-lung axis have direct correlations to immune bias that may promote chronic diseases like asthma. Asthma initiation and pathogenesis are multifaceted and complex with input from genetic, epigenetic, and environmental components. In this review, we summarize and discuss the role of the airway microbiome in asthma, and how the environment, diet and therapeutics impact this low biomass community of microorganisms. We also focus this review on the pediatric and Black populations as high-risk groups requiring special attention, emphasizing that the whole patient must be considered during treatment. Although new culture-independent techniques have been developed and are more accessible to researchers, the exact contribution the airway microbiome makes in asthma pathogenesis is not well understood. Understanding how the airway microbiome, as a living entity in the respiratory tract, participates in lung immunity during the development and progression of asthma may lead to critical new treatments for asthma, including population-targeted interventions, or even more effective administration of currently available therapeutics.

Physiological microbial exposure transiently inhibits mouse lung ILC2 responses to allergens

Lung group 2 innate lymphoid cells (ILC2s) control the nature of immune responses to airway allergens. Some microbial products, including those that stimulate interferons, block ILC2 activation, but whether this occurs after natural infections or causes durable ILC2 inhibition is unclear. In the present study, we cohoused laboratory and pet store mice as a model of physiological microbial exposure. Laboratory mice cohoused for 2 weeks had impaired ILC2 responses and reduced lung eosinophilia to intranasal allergens, whereas these responses were restored in mice cohoused for ≥2 months. ILC2 inhibition at 2 weeks correlated with increased interferon receptor signaling, which waned by 2 months of cohousing. Reinduction of interferons in 2-month cohoused mice blocked ILC2 activation. These findings suggest that ILC2s respond dynamically to environmental cues and that microbial exposures do not control long-term desensitization of innate type 2 responses to allergens.

The Influence of the Gut Microbiome in Paediatric Cancer Origin and Treatment

Knowledge of the complexity of the gut microbiota is expanding, and its importance in physiological processes and disease development is widely studied. The aim of this review is to present the most relevant and recent research on the associations between gut microbiota and oncologic disease. Recently, a number of associations between the gut microbiome and neoplasms—regarding tumorigenesis, prognosis and therapeutic efficacy—have been reported. The effects of the gut microbiome on these processes are via the direct and indirect immunomodulating effects of bacteria. Studies have been done mainly in adult populations, where its effect on immunomodulating therapies was unambiguous. In paediatric populations, however, due to the low number of cases and the complex therapeutic approaches, there have been only a few studies. Among them, children with acute lymphoblastic leukaemia were mainly involved. Significant alterations in the abundance of certain bacteria were associated with altered therapeutic responses. Regarding solid tumours, studies with low case numbers have been reported; no significant discoveries have been described so far. In the future, studies with larger cohorts are needed in order to better understand the associations between bacteria and neoplasms and to improve prognosis in the paediatric oncologic population.

The Microbiome as a Gateway to Prevention of Allergic Disease Development

Allergic diseases exclusively affect tissues that face environmental challenges and harbor endogenous bacterial microbiota. The microbes inhabiting the affected tissues may not be mere bystanders in this process but actively affect the risk of allergic sensitization, disease development, and exacerbation or abatement of symptoms. Experimental evidence provides several plausible means by which the human microbiota could influence the development of allergic diseases including, but not limited to, effects on antigen presentation and induction of tolerance and allergen permeation by endorsing or disrupting epithelial barrier integrity. Epidemiological evidence attests to the significance of age-appropriate, nonpathogenic microbiota development in skin, gastrointestinal tract, and airways for protection against allergic disease development. Thus, there exist potential targets for preventive actions either in the prenatal or postnatal period. These could include maternal dietary interventions, antibiotic stewardship for both the mother and infant, reducing elective cesarean deliveries, and understanding barriers to breastfeeding and timing of food diversification. In here, we will review the current understanding and evidence of allergy-associated human microbiota patterns, their role in the development of allergic diseases, and how we could harness these associations to our benefit against allergies.

Antibiotics in elderly Chinese population and their relations with hypertension and pulse pressure

Although antibiotic exposure in the general population has been well documented by a biomonitoring approach, epidemiologic data on the relationships between urinary antibiotic burden in the elderly with blood pressure (BP) are still lacking. The current study revealed thirty-four antibiotics in urine specimens from 990 elderly patients in Lu'an City, China, with detection frequencies ranging from 0.2 to 35.5%. Among the elderly, the prevalence of hypertension was 72.0%, and 12 antibiotics were detected in more than 10% of individuals with hypertension. The elderly with hypertension had the maximum daily exposure (5450.45 μg/kg/day) to fluoroquinolones (FQs). Multiple linear regression analyses revealed significant associations of BP and pulse pressure (PP) with exposure to specific antibiotics. The estimated β values (95% confidence interval) of associations with systolic blood pressure (SBP) in the right arm were 4.42 (1.15, 7.69) for FQs, 4.26 (0.52, 8.01) for the preferred as human antibiotics (PHAs), and 3.48 (0.20, 6.77) for the mixtures (FQs + tetracyclines [TCs] (tertile 3 vs. tertile 1)), respectively. Increased concentrations of TCs were associated with decreased diastolic BP (DBP; tertile 3: -1.75 [-3.39, -0.12]) for the right arm. Higher levels of FQs (tertile 3: 4.28 [1.02, 7.54]), PHAs (tertile 3: 4.25 [0.49, 8.01]), and FQs + TCs (tertile 3: 3.99 [0.71, 7.26]) were associated with increased SBP, and an increase in DBP for FQs (tertile 3: 1.82 [0.22, 3.42]) was shown in the left arm. Also, higher urinary concentrations of FQs (tertile 3: 3.18 [0.53, 5.82]), PHAs (tertile 3: 3.42 [0.40, 6.45]), and FQs + TCs (tertile 3: 3.06 [0.40, 5.72]) were related to increased PP, whereas a decline in PP for TCs (tertile 2: -2.93 [-5.60, -0.25]) in the right arm. And increased concentrations of penicillin V (tertile 3: 5.31 [1.53, 9.10]) and FQs + TCs (tertile 3: 2.84 [0.19, 5.49]) were related to higher PP in the left arm. By utilizing restricted cubic splines, our current study revealed a potential nonlinear dose-response association between FQ exposure and hypertension risk. In conclusion, this investigation is the first to present antibiotic exposure using a biomonitoring approach, and informs understanding of impacts of antibiotic residues, as emerging hazardous pollutants, on the hypertension risk in the elderly.

Controlling skin microbiome as a new bacteriotherapy for inflammatory skin diseases

The skin serves as the interface between the human body and the environment and interacts with the microbial community. The skin microbiota consists of microorganisms, such as bacteria, fungi, mites, and viruses, and they fluctuate depending on the microenvironment defined by anatomical location and physiological function. The balance of interactions between the host and microbiota plays a pivotal role in the orchestration of skin homeostasis; however, the disturbance of the balance due to an alteration in the microbial communities, namely, dysbiosis, leads to various skin disorders. Recent developments in sequencing technology have provided new insights into the structure and function of skin microbial communities. Based on high-throughput sequencing analysis, a growing body of evidence indicates that a new treatment using live bacteria, termed bacteriotherapy, is a feasible therapeutic option for cutaneous diseases caused by dysbiosis. In particular, the administration of specific bacterial strains has been investigated as an exclusionary treatment strategy against pathogens associated with chronic skin disorders, whereas the safety, efficacy, and sustainability of this therapeutic approach using isolated live bacteria need to be further explored. In this review, we summarize our current understanding of the skin microbiota, as well as therapeutic strategies using characterized strains of live bacteria for skin inflammatory diseases. The ecosystem formed by interactions between the host and skin microbial consortium is still largely unexplored; however, advances in our understanding of the function of the skin microbiota at the strain level will lead to the development of new therapeutic methods.

Mass drug administration of antibacterials: weighing the evidence regarding benefits and risks

Background

Mass drug administration (MDA) is a strategy to improve health at the population level through widespread delivery of medicine in a community. We surveyed the literature to summarize the benefits and potential risks associated with MDA of antibacterials, focusing predominantly on azithromycin as it has the greatest evidence base.

Main body

High-quality evidence from randomized controlled trials (RCTs) indicate that MDA-azithromycin is effective in reducing the prevalence of infection due to yaws and trachoma. In addition, RCTs suggest that MDA-azithromycin reduces under-five mortality in certain low-resource settings that have high childhood mortality rates at baseline. This reduction in mortality appears to be sustained over time with twice-yearly MDA-azithromycin, with the greatest effect observed in children < 1 year of age. In addition, observational data suggest that infections such as skin and soft tissue infections, rheumatic heart disease, acute respiratory illness, diarrheal illness, and malaria may all be treated by azithromycin and thus incidentally impacted by MDA-azithromycin. However, the mechanism by which MDA-azithromycin reduces childhood mortality remains unclear. Verbal autopsies performed in MDA-azithromycin childhood mortality studies have produced conflicting data and are underpowered to answer this question. In addition to benefits, there are several important risks associated with MDA-azithromycin. Direct adverse effects potentially resulting from MDA-azithromycin include gastrointestinal side effects, idiopathic hypertrophic pyloric stenosis, cardiovascular side effects, and increase in chronic diseases such as asthma and obesity. Antibacterial resistance is also a risk associated with MDA-azithromycin and has been reported for both gram-positive and enteric organisms. Further, there is the risk for cross-resistance with other antibacterial agents, especially clindamycin.

Conclusions

Evidence shows that MDA-azithromycin programs may be beneficial for reducing trachoma, yaws, and mortality in children < 5 years of age in certain under-resourced settings. However, there are significant potential risks that need to be considered when deciding how, when, and where to implement these programs. Robust systems to monitor benefits as well as adverse effects and antibacterial resistance are warranted in communities where MDA-azithromycin programs are implemented.

Graphical Abstract

Early-life exposure to antibiotics and subsequent development of atopic dermatitis

BACKGROUND

Antibiotic exposure may be associated with atopic dermatitis (AD). The objective of the study is to examine the risk of developing AD among children exposed early to antibiotics.

RESEARCH DESIGN AND METHODS

From the Italian Pedianet database, children aged 0-14 years between 2004-2017 were enrolled from birth up to at least one year. Cox proportional-hazards models were fitted to estimate Hazard Ratios (HR) and 95% Confidence Intervals (CI) for the association between antibiotic exposure during the first year of life with incident AD. Exposure was also considered as a time-varying variable.

RESULTS

73,816 children were included in the final cohort, of which 34,202 had at least one antibiotic prescription. Incident AD was present in 8% of unexposed and exposed children. Early antibiotic exposure was not associated with any excess risk of AD compared to unexposed children (HR: 1.02, 95% CI: 0.97-1.07), and no dose-response effect was observed. In the time-varying analysis, antibiotic exposure was significantly associated with AD onset (1.12, 1.07-1.17). However, when taking into account the time-lag between exposure and outcome, risks progressively decreased, suggesting possible protopathic bias.

CONCLUSION

These results are not suggestive of any significant association between exposure to antibiotics and subsequent AD onset and support the possible presence of protopathic bias.

Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life

The gastrointestinal microbiota begins to be acquired at birth and continually matures through early adolescence. Despite the relevance for gut health, few studies have evaluated the impact of pathobiont colonization of neonates on the severity of colitis later in life. LF82 is an adherent invasive E. coli strain associated with ileal Crohn’s disease. The aim of this study was to evaluate the severity of dextran sodium sulfate (DSS)-induced colitis in mice following E. coli LF82 colonization. Gnotobiotic mice harboring the altered Schaedler flora (ASF) were used as the model. While E. coli LF82 is neither adherent nor invasive, it was been demonstrated that adult ASF mice colonized with E. coli LF82 develop more severe DSS-induced colitis compared to control ASF mice treated with DSS. Therefore, we hypothesized that E. coli LF82 colonization of neonatal ASF mice would reduce the severity of DSS-induced inflammation compared to adult ASF mice colonized with E. coli LF82. To test this hypothesis, adult ASF mice were colonized with E. coli LF82 and bred to produce offspring (LF82_N) that were vertically colonized with LF82. LF82_N and adult-colonized (LF82_A) mice were given 2.0% DSS in drinking water for seven days to trigger colitis. More severe inflammatory lesions were observed in the LF82_N + DSS mice when compared to LF82_A + DSS mice, and were characterized as transmural in most of the LF82_N + DSS mice. Colitis was accompanied by secretion of proinflammatory cytokines (IFNγ, IL-17) and specific mRNA transcripts within the colonic mucosa. Using 16S rRNA gene amplicon sequencing, LF82 colonization did not induce significant changes in the ASF community; however, minimal changes in spatial redistribution by fluorescent in situ hybridization were observed. These results suggest that the age at which mice were colonized with E. coli LF82 pathobiont differentially impacted severity of subsequent colitic events.

Microbiome Modulation as a Novel Strategy to Treat and Prevent Respiratory Infections

Acute and chronic lower airway disease still represent a major cause of morbidity and mortality on a global scale. With the steady rise of multidrug-resistant respiratory pathogens, such as Pseudomonas aeruginosa and Klebsiella pneumoniae, we are rapidly approaching the advent of a post-antibiotic era. In addition, potentially detrimental novel variants of respiratory viruses continuously emerge with the most prominent recent example being severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this end, alternative preventive and therapeutic intervention strategies will be critical to combat airway infections in the future. Chronic respiratory diseases are associated with alterations in the lung and gut microbiome, which is thought to contribute to disease progression and increased susceptibility to infection with respiratory pathogens. In this review we will focus on how modulating and harnessing the microbiome may pose a novel strategy to prevent and treat pulmonary infections as well as chronic respiratory disease.

Asthma management in low- and middle-income countries: case for change

Asthma is the most common non-communicable disease in children, and among the most common in adults. The great majority of people with asthma live in low- and middle-income countries (LMICs), where they suffer disproportionately high asthma-related morbidity and mortality. Essential inhaled medications, particularly those containing inhaled corticosteroids (ICS), are often unavailable or unaffordable, and this explains much of the global burden of preventable asthma morbidity and mortality.Guidelines developed for LMICs are generally based on the outdated assumption that patients with asthma symptoms <1-3 times/week do not need (or benefit from) ICS. Even when ICS is prescribed, many patients manage their asthma with oral or inhaled short-acting beta₂ agonist (SABA) alone, due to issues of availability and affordability. A single ICS-formoterol inhaler-based approach to asthma management for all severities of asthma, from mild to severe, starting at diagnosis, might overcome SABA overuse/over-reliance and reduce the burden of symptoms and severe exacerbations. However, ICS-formoterol inhalers are currently very poorly available or unaffordable in LMICs. There is a pressing need for pragmatic clinical trial evidence of the feasibility and cost-effectiveness of this and other strategies to improve asthma care in these countries.The global health inequality in asthma care that deprives so many children, adolescents and adults of healthy lives and puts them at increased risk of death - despite the availability of highly effective therapeutic approaches - is unacceptable. A World Health Assembly Resolution on universal access to affordable effective asthma care is needed to focus attention and investment on addressing this need.

Antibiotic exposure and adverse long-term health outcomes in children: a systematic review and meta-analysis

BACKGROUND

Antibiotics are among the most commonly used drugs in children. In addition to inducing antibiotic resistance, antibiotic exposure has been associated with long-term adverse health outcomes.

METHODS

A systematic search using PRISMA Guidelines to identify original studies reporting associations between antibiotic exposure and long-term adverse health outcomes in children. Overall pooled estimates of the odds ratios (ORs) were obtained using fixed or random-effects models.

RESULTS

We identified 160 observational studies investigating 21 outcomes in 22,103,129 children. Antibiotic exposure was associated with an increased risk of atopic dermatitis (OR 1.40, 95% confidence interval (CI) 1.30-1.52, p<0.01), allergic symptoms (OR 1.93, 95%CI 1.66-2.26, p<0.01), food allergies (OR 1.35, 95%CI 1.20-1.52, p<0.01), allergic rhinoconjunctivitis (OR 1.66, 95%CI 1.51-1.83, p<0.01), wheezing (OR 1.81, 95%CI 1.65-1.97, p<0.01), asthma (OR 1.96, 95%CI 1.76-2.17, p<0.01), increased weight gain or overweight (OR 1.18, 95%CI 1.11-1.26, p<0.01), obesity (OR 1.21, 95%CI 1.05-1.40, p<0.01), juvenile idiopathic arthritis (OR 1.74, 95%CI 1.21-2.52, p<0.01), psoriasis (OR 1.75, 95%CI 1.44-2.11, p<0.01), autism spectrum disorders (OR 1.19, 95%CI 1.04-1.36, p=0.01) and neurodevelopment disorders (OR 1.29, 95%CI 1.09-1.53, p<0.01). Dose-response effects and stronger effects with broad-spectrum antibiotic were often reported. Antibiotic exposure was not associated with an altered risk of allergic sensitisation, infantile colic, abdominal pain, inflammatory bowel disease, celiac disease, type 1 diabetes, fluorosis, and attention deficit hyperactivity disorder.

CONCLUSION

Although a causal association cannot be determined from these studies, the results support the meticulous application of sound antibiotic stewardship to avoid potential adverse long-term health outcomes.

Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis

Antibiotics in childhood have been linked with diseases including asthma, juvenile arthritis, type 1 diabetes, Crohn's disease and mental illness. The underlying mechanisms are thought related to dysbiosis of the gut microbiome. We conducted a systematic review of the association between antibiotics and disruption of the pediatric gut microbiome. Searches used MEDLINE, EMBASE and Web of Science. Eligible studies: association between antibiotics and gut microbiome dysbiosis; children 0-18 years; molecular techniques of assessment; outcomes of microbiome richness, diversity or composition. Quality assessed by Newcastle-Ottawa Scale or Cochrane Risk of Bias Tool. Meta-analysis where possible. A total of 4,668 publications identified: 12 in final analysis (5 randomized controlled trials (RCTs), 5 cohort studies, 2 cross-sectional studies). Microbiome richness was measured in 3 studies, species diversity in 6, and species composition in 10. Quality of evidence was good or fair. 5 studies found a significant reduction in diversity and 3 a significant reduction in richness. Macrolide exposure was associated with reduced richness for twice as long as penicillin. Significant reductions were seen in Bifidobacteria (5 studies) and Lactobacillus (2 studies), and significant increases in Proteobacteria such as E. coli (4 studies). A meta-analysis of RCTs of the effect of macrolide (azithromycin) exposure on the gut microbiome found a significant reduction in alpha-diversity (Shannon index: mean difference -0.86 (95% CI -1.59, -0.13). Antibiotic exposure was associated with reduced microbiome diversity and richness, and with changes in bacterial abundance. The potential for dysbiosis in the microbiome should be taken into account when prescribing antibiotics for children.Systematic review registration number: CRD42018094188.

Factors Associated With Bronchiolitis Guideline Nonadherence at US Children's Hospitals

BACKGROUND

The objective with this study was to explore factors associated with nonadherence to national bronchiolitis guidelines at 52 children's hospitals.

METHODS

We included patients 1 month to 2 years old with emergency department (ED) or admission encounters between January 2016 and December 2018 and bronchiolitis diagnoses in the Pediatric Health Information System database. We excluded patients with any intensive care, stay >7 days, encounters in the preceding 30 days, chronic medical conditions, croup, pneumonia, or asthma. Guideline nonadherence was defined as receiving any of 5 tests or treatments: bronchodilators, chest radiographs, systemic steroids, antibiotics, and viral testing. Nonadherence outcomes were modeled by using mixed effects logistic regression with random effects for providers and hospitals. Adjusted odds ratio (aOR) >1 indicates greater likelihood of nonadherence.

RESULTS

A total of 198 028 encounters were included (141 442 ED and 56 586 admission), and nonadherence was 46.1% (ED: 40.2%, admissions: 61.0%). Nonadherence increased with patient age, with both ED and hospital providers being more likely to order tests and treatments for children 12 to 24 months compared with infants 1 ot 2 months (ED: aOR, 3.39; 95% confidence interval [CI], 3.20-3.60; admissions: aOR, 2.97; CI, 2.79-3.17]). Admitted non-Hispanic Black patients were more likely than non-Hispanic white patients to receive guideline nonadherent care (aOR, 1.16; CI, 1.10-1.23), a difference driven by higher use of steroids (aOR, 1.29; CI, 1.17-1.41) and bronchodilators (aOR, 1.39; CI, 1.31-1.48). Hospital effects were prominent for viral testing in ED and admission encounters (intraclass correlation coefficient of 0.35 and 0.32, respectively).

CONCLUSIONS

Multiple factors are associated with national bronchiolitis guideline nonadherence.

Racial and ethnic disparities in bronchiolitis management in freestanding children's hospitals

OBJECTIVE

Variation in bronchiolitis management by race and ethnicity within emergency departments (EDs) has been described in single-center and prospective studies, but large-scale assessments across EDs and inpatient settings are lacking. Our objective is to describe the association between race and ethnicity and bronchiolitis management across 37 U.S. freestanding children's hospitals from 2015 to 2018.

METHODS

Using the Pediatric Health Information System, we analyzed ED and inpatient visits from November 2015 to November 2018 of children with bronchiolitis 3 to 24 months old. Rates of use for specific diagnostic tests and therapeutic measures were compared across the following race/ethnicity categories: 1) non-Hispanic White (NHW), 2) non-Hispanic Black (NHB), 3) Hispanic, and 4) other. The subanalyses of ED patients only and children < 1 year old were performed. Mixed-effect logistic regression was performed to compare the adjusted odds of receiving specific test/treatment using NHW children as the reference group.

RESULTS

A total of 134,487 patients met inclusion criteria (59% male, 28% NHB, 26% Hispanic). Adjusted analysis showed that NHB children had higher odds of receiving medication associated with asthma (odds ratio [OR] = 1.27, 95% confidence interval [CI] = 1.22 to 1.32) and lower odds of receiving diagnostic tests (blood cultures, complete blood counts, viral testing, chest x-rays; OR = 0.78, 95% CI = 0.75 to 0.81) and antibiotics (OR = 0.58, 95% CI = 0.52 to 0.64) than NHW children. Hispanic children had lower odds of receiving diagnostic testing (OR = 0.94, 95% CI = 0.90 to 0.98), asthma-associated medication (OR = 0.92, 95% CI = 0.88 to 0.96), and antibiotics (OR = 0.74, 95% CI = 0.66 to 0.82) compared to NHW children.

CONCLUSION

NHB children more often receive corticosteroid and bronchodilator therapies; NHW children more often receive antibiotics and chest radiography. Given that current guidelines generally recommend supportive care with limited diagnostic testing and medical intervention, these findings among NHB and NHW children represent differing patterns of overtreatment. The underlying causes of these patterns require further investigation.

Big Data, Data Science, and Causal Inference: A Primer for Clinicians

Clinicians handle a growing amount of clinical, biometric, and biomarker data. In this “big data” era, there is an emerging faith that the answer to all clinical and scientific questions reside in “big data” and that data will transform medicine into precision medicine. However, data by themselves are useless. It is the algorithms encoding causal reasoning and domain (e.g., clinical and biological) knowledge that prove transformative. The recent introduction of (health) data science presents an opportunity to re-think this data-centric view. For example, while precision medicine seeks to provide the right prevention and treatment strategy to the right patients at the right time, its realization cannot be achieved by algorithms that operate exclusively in data-driven prediction modes, as do most machine learning algorithms. Better understanding of data science and its tasks is vital to interpret findings and translate new discoveries into clinical practice. In this review, we first discuss the principles and major tasks of data science by organizing it into three defining tasks: (1) association and prediction, (2) intervention, and (3) counterfactual causal inference. Second, we review commonly-used data science tools with examples in the medical literature. Lastly, we outline current challenges and future directions in the fields of medicine, elaborating on how data science can enhance clinical effectiveness and inform medical practice. As machine learning algorithms become ubiquitous tools to handle quantitatively “big data,” their integration with causal reasoning and domain knowledge is instrumental to qualitatively transform medicine, which will, in turn, improve health outcomes of patients.

Antibiotic Treatments During Infancy, Changes in Nasal Microbiota, and Asthma Development: Population-based Cohort Study

Background

Early-life exposures to antibiotics may increase the risk of developing childhood asthma. However, little is known about the mechanisms linking antibiotic exposures to asthma. We hypothesized that changes in the nasal airway microbiota serve as a causal mediator in the antibiotics–asthma link.

Methods

In a population-based birth-cohort study in Finland, we identified longitudinal nasal microbiota profiles during age 2–24 months using 16S rRNA gene sequencing and an unsupervised machine learning approach. We performed a causal mediation analysis to estimate the natural direct effect of systemic antibiotic treatments during age 0–11 months on risks of developing physician-diagnosed asthma by age 7 years and the natural indirect (causal mediation) effect through longitudinal changes in nasal microbiota.

Results

In our birth cohort of 697 children, 8.0% later developed asthma. Exposure to ≥2 antibiotic treatments during age 0–11 months was associated with a 4.0% increase in the absolute risk of developing asthma (absolute increase, 95% CI, .9–7.2%; P = .006). The unsupervised clustering approach identified 6 longitudinal nasal microbiota profiles. Infants with a larger number of antibiotic treatments had a higher risk of having a profile with early Moraxella sparsity (per each antibiotic treatment, adjusted RRR, 1.38; 95% CI, 1.15–1.66; P < .001). This effect of antibiotics on asthma was partly mediated by longitudinal changes in the nasal microbiota (natural indirect effect, P = .008), accounting for 16% of the total effect.

Conclusions

Early exposures to antibiotics were associated with increased risk of asthma; the effect was mediated, in part, by longitudinal changes in the nasal airway microbiota.

[Cultivation and use of medicinal plants and association with reporting of childhood asthma: A case-control study in the Bogotá savanna]

Introduction

The prevalence of childhood asthma has increased in recent years. The World Health Organization has called for conducting research exploring the role of traditional medicine and medicinal plants in respiratory disease control.

Objective

To identify the relationship between the prevalence of childhood asthma and traditional care of the respiratory system, including cultivation and use of medicinal plants.

Methods

We conducted an observational, analytic, case-control study that included children 2 to 14 years old who used official health services in eight municipalities near Bogota between 2014 and 2015. Cases were children diagnosed with asthma. We randomly selected the controls among the remaining patients of the same healthcare facilities. We applied an 18-question survey. The Mantel-Haenszel procedure identified significant associations using 95% confidence intervals.

Results

We surveyed the caretakers of 97 cases and 279 controls in eight municipalities. Some 23.4% (88/376) and 37.9% (142/375) reported using traditional remedies for fever control and common cold management, respectively. 8.8% (33/376) reported following traditional care during a common cold, 30.4% (114/375) reported growing medicinal plants at home, and 45% (166/369) reported using medicinal plants for health purposes in their household. Multivariate analysis showed that having and using medicinal plants at home is associated with a lower reporting of asthma (odds ratio 0.49; 95% confidence interval: 0.25 to 0.99).

Conclusions

Cultivating and using medicinal plants at home is associated with a lower reporting of childhood asthma. Researchers should consider the therapeutic, environmental, and cultural properties of medicinal plants to prevent respiratory diseases.

Vaccines for multidrug resistant Gram negative bacteria: lessons from the past for guiding future success

Antimicrobial resistance is a major threat to global public health. Vaccination is an effective approach for preventing bacterial infections, however it has not been successfully applied to infections caused by some of the most problematic multidrug resistant pathogens. In this review, the potential for vaccines to contribute to reducing the burden of disease of infections caused by multidrug resistant Gram negative bacteria is presented. Technical, logistical and societal hurdles that have limited successful vaccine development for these infections in the past are identified, and recent advances that can contribute to overcoming these challenges are assessed. A synthesis of vaccine technologies that have been employed in the development of vaccines for key multidrug resistant Gram negative bacteria is included, and emerging technologies that may contribute to future successes are discussed. Finally, a comprehensive review of vaccine development efforts over the last 40 years for three of the most worrisome multidrug resistant Gram negative pathogens, Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa is presented, with a focus on recent and ongoing studies. Finally, future directions for the vaccine development field are highlighted.

Maternal antibiotic exposure during pregnancy and the risk of allergic diseases in childhood: A meta-analysis

BACKGROUND

Increasing studies suggest that antibiotic exposure during pregnancy may increase the risk of childhood allergic diseases; however, controversy still exists. Thus, we conducted this meta-analysis to evaluate the association between antibiotic use during pregnancy and childhood asthma/wheeze, eczema/atopic dermatitis, and food allergy.

METHODS

CENTRAL, EMBASE, and PubMed were searched for studies up to July 20, 2020. Cohort studies and case-control studies that estimated the association of antibiotic exposure in pregnancy with the risk of childhood asthma/wheeze, eczema/atopic dermatitis, and food allergy were included. A random-effects model or fixed-effects model was used to calculate the pooled estimates. The quality of the included studies was assessed by the Newcastle-Ottawa Scale (NOS). Stata12.0 software was used to analyze the association through a meta-analysis.

RESULTS

A total of 26 studies were included in the meta-analysis. The results showed that maternal antibiotic exposure in pregnancy and the summary OR for the risk of childhood asthma/wheeze was 1.29 (95% CI = 1.16-1.43), the summary OR for eczema/atopic dermatitis was 1.62 (95% CI = 1.16-2.27), and the pooled OR for food allergy was 1.36 (95% CI = 0.94-1.96).

CONCLUSIONS

Our results indicated that maternal antibiotic use during pregnancy might increase the risk of asthma/wheeze and eczema/atopic dermatitis but not food allergy in children. Further studies with larger sample size and robust multivariable adjustment are needed to confirm our findings. Nevertheless, the appropriate use of antibiotics during pregnancy is incredibly important, and healthcare professionals should be selective when prescribing antibiotics for pregnant women.

Association of Early Life Exposure to Antibiotics With Risk of Atopic Dermatitis in Sweden

IMPORTANCE

Atopic dermatitis is associated with substantial morbidity in childhood. Further understanding of the underlying factors contributing to its onset is needed.

OBJECTIVE

To assess the association of exposure to antibiotics in the prenatal period and early childhood with risk of atopic dermatitis in a nationwide population in Sweden.

DESIGN, SETTING, AND PARTICIPANTS

This Swedish nationwide, register-based, prospective cohort study used data on mother-child pairs from the Swedish Medical Birth Register linked to other national registers for information on health, socioeconomic, and demographic data. Participants were followed up until an atopic dermatitis outcome, emigration, death, or the end of the study on December 31, 2015. Data for all singleton children and discordant siblings born between March 1, 2006, and December 31, 2010, were included. Data were analyzed from June 1, 2020, to October 31, 2020.

EXPOSURES

Maternal exposure to systemic antibiotics during pregnancy as well as the child's exposure to systemic antibiotics during the first year of life, as defined by a dispensed prescription in the Swedish Prescribed Drug Register.

MAIN OUTCOMES AND MEASURES

Time-to-event analyses were used to estimate the risk of outcome using attained age as a time scale. Atopic dermatitis was defined based on diagnoses in the National Patient Register and medication listed in the Swedish Prescribed Drug Register. Sibling-control analysis was performed to account for shared familial factors.

RESULTS

Among the 722 767 singleton children, the mean (SD) age was 5.8 (2.4) years and 351 589 (48.6%) were female. During the follow-up period, 153 407 children (21.2%) were exposed to antibiotics in utero and 172 405 children (23.8%) were exposed during the first year of life. The risk of atopic dermatitis among children exposed to prenatal antibiotics was greater than that among children who were not exposed (adjusted hazard ratio [aHR], 1.10; 95% CI, 1.09-1.12). In the sibling-control analysis, no association was observed (aHR, 0.96; 95% CI; 0.92-1.00). Exposure to antibiotics during the first year of life was associated with a greater risk of atopic dermatitis (aHR, 1.52; 95% CI, 1.50-1.55), with attenuated associations in the sibling-control analysis (aHR, 1.24; 95% CI, 1.20-1.29).

CONCLUSIONS AND RELEVANCE

In this cohort study, exposure to antibiotics in early life was associated with an increased risk of atopic dermatitis in the general Swedish population, but this risk was partially confounded by familial factors. Research on the ways in which antibiotic use and other shared familial factors affect other atopic diseases may be warranted.

A modular approach to integrating multiple data sources into real-time clinical prediction for pediatric diarrhea

Traditional clinical prediction models focus on parameters of the individual patient. For infectious diseases, sources external to the patient, including characteristics of prior patients and seasonal factors, may improve predictive performance. We describe the development of a predictive model that integrates multiple sources of data in a principled statistical framework using a post-test odds formulation. Our method enables electronic real-time updating and flexibility, such that components can be included or excluded according to data availability. We apply this method to the prediction of etiology of pediatric diarrhea, where 'pre-test’ epidemiologic data may be highly informative. Diarrhea has a high burden in low-resource settings, and antibiotics are often over-prescribed. We demonstrate that our integrative method outperforms traditional prediction in accurately identifying cases with a viral etiology, and show that its clinical application, especially when used with an additional diagnostic test, could result in a 61% reduction in inappropriately prescribed antibiotics.

Early-life EV-A71 infection augments allergen-induced airway inflammation in asthma through trained macrophage immunity

Virus-induced asthma is prevalent among children, but its underlying mechanisms are unclear. Accumulated evidence indicates that early-life respiratory virus infection increases susceptibility to allergic asthma. Nonetheless, the relationship between systemic virus infections, such as enterovirus infection, and the ensuing effects on allergic asthma development is unknown. Early-life enterovirus infection was correlated with higher risks of allergic diseases in children. Adult mice exhibited exacerbated mite allergen-induced airway inflammation following recovery from EV-A71 infection in the neonatal period. Bone marrow-derived macrophages (BMDMs) from recovered EV-A71-infected mice showed sustained innate immune memory (trained immunity) that could drive naïve T helper cells toward Th2 and Th17 cell differentiation when in contact with mites. Adoptive transfer of EV-A71-trained BMDMs induced augmented allergic inflammation in naïve recipient mice, which was inhibited by 2-deoxy-D-glucose (2-DG) pretreatment, suggesting that trained macrophages following enterovirus infection are crucial in the progression of allergic asthma later in life.

The Association between Early-Life Gut Microbiota and Long-Term Health and Diseases

Early life gut microbiota have been increasingly recognized as major contributors to short and/or long-term human health and diseases. Numerous studies have demonstrated that human gut microbial colonization begins at birth, but continues to develop a succession of taxonomic abundances for two to three years until the gut microbiota reaches adult-like diversity and proportions. Several factors, including gestational age (GA), delivery mode, birth weight, feeding types, antibiotic exposure, maternal microbiome, and diet, influence the diversity, abundance, and function of early life gut microbiota. Gut microbial life is essential for assisting with the digestion of food substances to release nutrients, exerting control over pathogens, stimulating or modulating the immune system, and influencing many systems such as the liver, brain, and endocrine system. Microbial metabolites play multiple roles in these interactions. Furthermore, studies provide evidence supporting that imbalances of the gut microbiota in early life, referred to as dysbiosis, are associated with specific childhood or adult disease outcomes, such as asthma, atopic dermatitis, diabetes, allergic diseases, obesity, cardiovascular diseases (CVD), and neurological disorders. These findings support that the human gut microbiota may play a fundamental role in the risk of acquiring diseases that may be programmed during early life. In fact, it is critical to explore the role of the human gut microbiota in early life.

Gut Microbiota Influence in Hematological Malignancies: From Genesis to Cure

Hematological malignancies, including multiple myeloma, lymphoma, and leukemia, are a heterogeneous group of neoplasms that affect the blood, bone marrow, and lymph nodes. They originate from uncontrolled growth of hematopoietic and lymphoid cells from different stages in their maturation/differentiation and account for 6.5% of all cancers around the world. During the last decade, it has been proven that the gut microbiota, more specifically the gastrointestinal commensal bacteria, is implicated in the genesis and progression of many diseases. The immune-modulating effects of the human microbiota extend well beyond the gut, mostly through the small molecules they produce. This review aims to summarize the current knowledge of the role of the microbiota in modulating the immune system, its role in hematological malignancies, and its influence on different therapies for these diseases, including autologous and allogeneic stem cell transplantation, chemotherapy, and chimeric antigen receptor T cells.

The Fungal Microbiome and Asthma

Asthma is a group of inflammatory conditions that compromises the airways of a continuously increasing number of people around the globe. Its complex etiology comprises both genetic and environmental aspects, with the intestinal and lung microbiomes emerging as newly implicated factors that can drive and aggravate asthma. Longitudinal infant cohort studies combined with mechanistic studies in animal models have identified microbial signatures causally associated with subsequent asthma risk. The recent inclusion of fungi in human microbiome surveys has revealed that microbiome signatures associated with asthma risk are not limited to bacteria, and that fungi are also implicated in asthma development in susceptible individuals. In this review, we examine the unique properties of human-associated and environmental fungi, which confer them the ability to influence immune development and allergic responses. The important contribution of fungi to asthma development and exacerbations prompts for their inclusion in current and future asthma studies in humans and animal models.

The impact of early life antibiotic use on atopic and metabolic disorders: Meta-analyses of recent insights

Background and objectives

The impact of antibiotics use early in life on later-in-life morbidities has received substantial attention as explanations for atopic and metabolic disorders with a surge as modern lifestyle diseases. The objective of this study was to perform meta-analyses to determine if antibiotics administration during the first 2 years of infant life is associated with increased risks of atopic or metabolic disorders later in life.

Methodology

We screened more than 100 English-language prospective and retrospective studies published between January 2002 and March 2020 and assessed study quality using the Newcastle–Ottawa scale. We performed overall and subgroup meta-analyses on 31 high-quality comparable studies on atopic and 23 on metabolic disorders, involving more than 3.5 million children.

Results

Antibiotic exposure prenatally and during the first 2 years of life significantly impacts the risk of developing atopic and metabolic disorders. Exposure during the first 6 months of life appears most critical, consistent with this being the time when the microbiome is most susceptible to irreversible perturbations. The presence of dose−response associations and stronger impacts of broad- than narrow-spectrum antibiotics further point to effects being mediated by microbiota-induced changes.

Conclusions and implications

Our findings support that antibiotics use is a mismatch to modernity that can negatively affect the symbiotic associations we rely on for proper immune function and metabolism. Improving our understanding of these associations, the underlying proximate mechanisms and the impact of antibiotics use on future human−symbiont evolution will be important to improve human health.

Lay Summary

The use of antibiotics in infancy has been suggested to increase the risks of atopic and metabolic disorders later in life. Through meta-analyses of more than 100 studies of >3.5 million children, we confirm these risks, and show that patterns are consistent with effects being due to microbiota-driven changes.