Comparing the Etiology of Viral Acute Respiratory Illnesses Between Children Who Do and Do Not Attend Childcare.

BACKGROUND AND OBJECTIVE: Childcare attendance is a common risk factor for acute respiratory illness (ARI) in young children. Our goal was to better understand the specific respiratory viruses that predominate in childcare, which may support the development of tailored illness prevention and intervention strategies in childcare settings. METHODS: Using data from a prospective household cohort of ARI surveillance, we assessed specimen from 1418 ARIs reported by 359 childcare-aged children over 6 study seasons (2012/2013 through 2017/2018). Respiratory swabs were tested by polymerase chain reaction for 9 respiratory viruses. A mixed-effect logistic regression model was used to compare odds of various viral detection outcomes. The Shannon's Diversity index was used to compare the richness (ie, number of species) and diversity (ie, relative species abundance) associated with respiratory viruses detected in both groups. RESULTS: At least 1 virus was detected in 75.5% of childcare-associated ARIs and in 80.1% of homecare ARIs. Compared with illnesses among homecare children, childcare illnesses were associated with significantly higher odds of detected adenovirus (odds ratio = 1.86, 95% confidence interval = 1.05-3.28) and human metapneumovirus (odds ratio = 1.76, 95% confidence interval = 1.03-3.0). The pool of viruses associated with childcare ARI was found to be significantly richer and more diverse than that of viruses associated with homecare ARI ( P < 0.0001). CONCLUSIONS: Children attending childcare experience a higher risk of adenovirus and human metapneumovirus infection and are regularly exposed to a rich and diverse pool of respiratory viruses in childcare environments. Our results underscore the necessity of thorough and multifaceted viral prevention strategies in childcare settings.

Environmental predictors of pulmonary nontuberculous mycobacteria (NTM) sputum positivity among persons with cystic fibrosis in the state of Florida.

Nontuberculous mycobacteria (NTM) are opportunistic human pathogens that are commonly found in soil and water, and exposure to these organisms may cause pulmonary nontuberculous mycobacterial disease. Persons with cystic fibrosis (CF) are at high risk for developing pulmonary NTM infections, and studies have shown that prolonged exposure to certain environments can increase the risk of pulmonary NTM. It is therefore important to determine the risk associated with different geographic areas. Using annualized registry data obtained from the Cystic Fibrosis Foundation Patient Registry for 2010 through 2017, we conducted a geospatial analysis of NTM infections among persons with CF in Florida. A Bernoulli model in SaTScan was used to identify clustering of ZIP codes with higher than expected numbers of NTM culture positive individuals. Generalized linear mixed models with a binomial distribution were used to test the association of environmental variables and NTM culture positivity. We identified a significant cluster of M. abscessus and predictors of NTM sputum positivity, including annual precipitation and soil mineral levels.

Associations Between Salivary Bacteriome Diversity and Salivary Human Herpesvirus Detection in Early Childhood: A Prospective Cohort Study.

BACKGROUND: The bacteriome is associated with susceptibility to some eukaryotic viruses, but no study has examined associations between the salivary bacteriome and human herpesviruses (HHVs). We provide new prevalence and incidence estimates for salivary herpesviruses detection and estimate associations with bacteriome diversity in young children. METHODS: Salivary samples collected at ages ~2, 8, 12, and 24 months from 153 children participating in the Center for Oral Health Research in Appalachia cohort 2 (COHRA2) were screened for HHVs using the Fast-Track Neuro9 multiplex PCR assay, and for the bacteriome using 16S rRNA amplicon sequencing. We used Cox proportional hazard models to test for associations between the salivary bacteriome and hazards of cytomegalovirus (CMV) and human herpesvirus-6 (HHV6). RESULTS: CMV, HHV6, and Epstein-Barr virus (EBV) were detected at all visits. Human herpesvirus-7 (HHV7) was first detected at the 8-month visit and herpes simplex virus 1 (HSV1) was only detected at the 12-month visit. Varicella-zoster virus, herpes simplex virus 2, and human herpesvirus-8 were never detected. HHV6 (24-month cumulative incidence: 73.8%) and CMV (24-month cumulative incidence: 32.3%) were detected most frequently. Increasing salivary bacteriome diversity was associated with longer survival to first detection of CMV (hazard ratio [95% CI]: 0.24 [0.12, 0.49]) and HHV6 (hazard ratio [95% CI]: 0.24 [0.13, 0.44]). CONCLUSION: CMV, HHV6, EBV, HHV7, and HSV1 were detected in the saliva during the first 2 years of life. Time to first detection of CMV and HHV6 was associated with salivary bacteriome diversity, suggesting a possible interaction between HHVs and the salivary bacteriome.

Parsing Immune Correlates of Protection Against SARS-CoV-2 from Biomedical Literature.

After the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019, identification of immune correlates of protection (CoPs) have become increasingly important to understand the immune response to SARS-CoV-2. The vast amount of preprint and published literature related to COVID-19 makes it challenging for researchers to stay up to date on research results regarding CoPs against SARS-CoV-2. To address this problem, we developed a machine learning classifier to identify papers relevant to CoPs and a customized named entity recognition (NER) model to extract terms of interest, including CoPs, vaccines, assays, and animal models. A user-friendly visualization tool was populated with the extracted and normalized NER results and associated publication information including links to full-text articles and clinical trial information where available. The goal of this pilot project is to provide a basis for developing real-time informatics platforms that can inform researchers with scientific insights from emerging research.

Heterotypic Infection and Spread of Rhinovirus A, B, and C among Childcare Attendees.

Background: Despite the frequency of human rhinovirus (HRV), data describing the molecular epidemiology of HRV in the community are limited. Childcare centers are optimal settings to characterize heterotypic HRV cocirculation. Methods: HRV specimens were prospectively obtained from a cohort of childcare attendees at enrollment and weekly during respiratory illness. The 5' noncoding region sequences were used to determine HRV species (A, B, C) and genotypes. Results: Among 225 children followed, sequence data were available for 92 HRV infections: HRV-A (n = 80; 59%) was most common, followed by HRV-C (n = 52, 39%), and HRV-B (n = 3, 2%). Forty-one genotypes were identified and cocirculation was common. Frequent spread between classrooms occurred with 2 HRV-A genotypes. Repeated detections within single illnesses were a combination of persistent (n = 7) and distinct (n = 7) genotypes. Prevalence of HRV among asymptomatic children was 41%. HRV-C was clinically similar to HRV-A and HRV-B. Conclusions: HRV epidemiology in childcare consists of heterotypic cocirculation of genotypes with periodic spread within and among classrooms. Based on our finding of multiple genotypes evident during the course of single illnesses, the use of sequence-based HRV type determination is critical in longitudinal studies of HRV epidemiology and transmission.