Clinical Impact of Multiplex Molecular Diagnostic Testing in Children With Acute Gastroenteritis Presenting to an Emergency Department: A Multicenter Prospective Study.

BACKGROUND: Multiplex molecular diagnostic panels have greatly enhanced detection of gastrointestinal pathogens. However, data on the impact of these tests on clinical and patient-centered outcomes are limited. METHODS: We conducted a prospective, multicenter, stepped-wedge trial to determine the impact of multiplex molecular testing at 5 academic children's hospitals on children presenting to the emergency department with acute gastroenteritis. Caregivers were interviewed on enrollment and 7-10 days after enrollment to determine symptoms, risk factors, subsequent medical visits, and impact on family members. During the pre-intervention period, diagnostic testing was performed at the clinician's discretion . During the intervention period, multiplex molecular testing was performed on all children, with results available to clinicians. The primary outcome was return visits to a healthcare provider within 10 days of enrollment. RESULTS: Potential pathogens were identified by clinician-ordered tests in 19 of 571 (3.3%) in the pre-intervention period compared with 434 of 586 (74%) in the intervention period; clinically relevant pathogens were detected in 2.1% and 15%, respectively. In the multivariate model, the intervention was associated with a 21% reduction in the odds of any return visit (odds ratio, 0.79; 95% confidence interval, .70-.90) after adjusting for potential confounders. Appropriate treatment was prescribed in 11.3% compared with 19.6% during the intervention period (P = .22). CONCLUSIONS: Routine molecular multiplex testing for all children who presented to the ED with acute gastroenteritis detected more clinically relevant pathogens and led to a 21% decrease in return visits. Additional research is needed to define patients most likely to benefit from testing. Clinical Trials Registration. NCT02248285.

Clinical Impact of Multiplex Molecular Diagnostic Testing in Children with Acute Gastroenteritis Presenting to An Emergency Department: A Multicenter Prospective Study.

Background: Multiplex molecular diagnostic panels have greatly enhanced detection of gastrointestinal pathogens. However, data on the impact of these tests on clinical and patient-centered outcomes are limited. Methods: We conducted a prospective, multicenter, stepped-wedge trial to determine the impact of multiplex molecular testing at five academic children's hospitals in children presenting to the ED with acute gastroenteritis. Caregivers were interviewed on enrollment and again 7-10 days after enrollment to determine symptoms, risk factors, subsequent medical visits, and impact on family members. During the pre-intervention period, diagnostic testing was performed at the discretion of clinicians. During the intervention period, multiplex molecular testing was performed on all children with results available to clinicians. Primary outcome was return visits to a health care provider within 10 days of enrollment. Results: Potential pathogens were identified by clinician ordered tests in 19/571 (3.3%) in the pre-intervention period compared to 434/586 (74%) in the intervention period; clinically relevant pathogens were detected in 2.1% and 15% respectively. In the multivariate model adjusting for potential confounders, the intervention was associated with a 21% reduction in the odds of any return visit (OR 0.79; 95% CI 0.70-0.90). Appropriate treatment was prescribed in 11.3% compared to 19.6% during the intervention period(P=0.22). Conclusions: Routine molecular multiplex testing for all children presenting to the ED with AGE detected more clinically relevant pathogens and led to a 21% decrease in return visits. Additional research is needed to define patients most likely to benefit from testing.

Variation in Treatment of Pediatric Tuberculosis Infection in Different Provider Settings.

OBJECTIVES: To evaluate implementation of rifamycin-based regimens (RBR) for pediatric tuberculosis infection (TBI) treatment among 3 provider settings in a high-incidence county. STUDY DESIGN: A multicenter, retrospective observational study was performed across 3 sites in Los Angeles County: an academic center (AC), a general pediatrics federally qualified health center (FQHC), and department of public health (DPH) tuberculosis clinics. Patients initiated on TBI treatment age 1 months to 17 years between 2018 and 2020 were included. RBRs were defined as regimens: 3 months of weekly rifapentine and isoniazid, 4 months of daily rifampin, and 3 months of daily isoniazid and rifampin. RESULTS: We included 424 patients: 51 from AC, 327 from DPH, and 46 from FQHC. RBR use nearly doubled during the study period (from 43% in 2018 to 82% in 2020; P < .001). FQHC had the shortest time to chest radiograph and treatment initiation; however, AC and DPH were 4 times as likely to prescribe an RBR compared to FQHC (95% CI, 2.1-7.8). AC and DPH had similar completion rates (74%) and were 2.6 times as likely to complete treatment compared to FQHC (95% CI, 1.4-4.9). CONCLUSIONS: The use of RBRs for pediatric TBI varies significantly by clinical setting but is improving over time. Strategies are needed to improve RBR uptake, standardize care, and increase treatment completion, particularly among general pediatricians.

Coronavirus Disease 2019 Vaccine Booster Effects Are Seen in Human Milk Antibody Response.

Infants remain at high risk for severe coronavirus disease 2019 (COVID-19). Human milk contains high levels of protective SARS CoV-2 specific antibodies post-infection and primary vaccine series, but levels decline over time. We hypothesized that the COVID-19 booster vaccine augment antibody production and the protection afforded to human milk-fed infants. We prospectively enrolled pregnant or lactating mothers planning to receive COVID-19 vaccination. We measured human milk IgG, IgA, and IgM antibodies targeting the SARS CoV-2 receptor binding domain within the spike protein and human milk neutralization activity against SARS CoV-2 in 10 lactating mothers from pre-COVID-19 primary series vaccine to post-booster dose. Human milk SARS CoV-2 specific IgG increased significantly from pre- to post-booster levels (median OD 0.33 vs. 2.02, P = 0.002). The IgG levels post-booster were even higher than the peak level after the primary series (2.02 vs. 0.95, P = 0.03). The increase in SARS CoV-2 specific IgA levels was not significant (0.10 vs. 0.33, P = 0.23). There was a strong correlation between paired maternal blood and milk IgG and IgA levels (IgG rho 0.52, P < 0.001, IgA rho 0.31, P = 0.05). Post-booster neutralizing activity was elevated compared to pre-booster levels (66% vs. 12% inhibition, P = 0.002). COVID-19 vaccine booster elicits SARS CoV-2 specific antibodies in human milk at higher levels compared to the initial primary series. This finding suggests that three doses of COVID-19 mRNA vaccination leads to improved mucosal response in human milk and reinforces current guidance recommending all pregnant or lactating mothers receive full COVID-19 vaccine courses with a booster dose.

A Longitudinal Study of Assisted Infant Toilet Training During the First Year of Life.

OBJECTIVE: Previous retrospective studies have examined elimination signals, stool toileting refusal, and completion age in Assisted Infant Toilet Training (AITT). The aim of this longitudinal cohort study was to describe the practice of AITT and caregiver satisfaction in a primarily Western setting during the first year of life. METHODS: Families who started AITT before 4 months of age were recruited. Standardized interviews of caregivers were conducted at 1- to 2-month intervals. To identify trends over time, data were fitted to a linear mixed-effect model. Data were analyzed according to five 2-month blocks, starting at 3 to 4 months. RESULTS: Of 85 participating families, 87 children started AITT at a mean age of 2.5 months. At all age intervals, 88% to 94% of caregivers could identify elimination signals. Toileting attempts decreased from 10/day at 3 to 4 months to 7/day at 11 to 12 months (p < 0.001). Many families (45%-53%) practiced AITT on a part-time basis. Daytime dryness was noted in 12% to 14% of infants throughout the first year. Although more than 63% of families used cloth or disposable diapers throughout this study, use of trainers and underwear increased significantly by 2- to 3-fold (p < 0.01 for both). Caregiver satisfaction was high overall. Although negatively associated with potty refusal, it was positively associated with daytime and nighttime dryness, perceived elimination signals, and a better understanding of their infant's needs (p < 0.001 for all). CONCLUSION: This study demonstrates that AITT is a worthy viable alternative to the use of diapers even in Western settings. Better understanding of AITT provides a new perspective to properly meet infants' basic needs.

High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19.

BACKGROUND: The full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical characteristics in children. METHODS: Whole-genome sequencing was performed on respiratory specimens collected for all SARS-CoV-2-positive children (n = 141) between March 13 and June 16, 2020. Viral genetic variations across the SARS-CoV-2 genome were identified and investigated to evaluate genomic correlates of disease severity. RESULTS: Higher viral load was detected in symptomatic patients (P = .0007) and in children <5 years old (P = .0004). Genomic analysis revealed a mean pairwise difference of 10.8 single nucleotide variants (SNVs), and the majority (55.4%) of SNVs led to an amino acid change in the viral proteins. The D614G mutation in the spike protein was present in 99.3% of the isolates. The calculated viral mutational rate of 22.2 substitutions/year contrasts the 13.5 substitutions/year observed in California isolates without the D614G mutation. Phylogenetic clade 20C was associated with severe cases of COVID-19 (odds ratio, 6.95; P = .0467). Epidemiological investigation revealed major representation of 3 of 5 major Nextstrain clades (20A, 20B, and 20C) consistent with multiple introductions of SARS-CoV-2 in Southern California. CONCLUSIONS: Genomic evaluation demonstrated greater than expected genetic diversity, presence of the D614G mutation, increased mutation rate, and evidence of multiple introductions of SARS-CoV-2 into Southern California. Our findings suggest a possible association of phylogenetic clade 20C with severe disease, but small sample size precludes a definitive conclusion. Our study warrants larger and multi-institutional genomic evaluation and has implications for infection control practices.

Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome.

INTRODUCTION: The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time. MATERIALS AND METHODS: Stool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed. RESULTS: A total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA R2 = 0.044, p = .002) but later courses did not (R2 = 0.023, p = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray-Curtis distance 0.29 vs. 0.63, Wilcoxon p = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (p < .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome. CONCLUSION: Through this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in Escherichia coli. Further characterization of the infant mycobiome is still needed.

Comparison of Upper Respiratory Viral Load Distributions in Asymptomatic and Symptomatic Children Diagnosed with SARS-CoV-2 Infection in Pediatric Hospital Testing Programs.

The distribution of upper respiratory viral loads (VL) in asymptomatic children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown. We assessed PCR cycle threshold (Ct) values and estimated VL in infected asymptomatic children diagnosed in nine pediatric hospital testing programs. Records for asymptomatic and symptomatic patients with positive clinical SARS-CoV-2 tests were reviewed. Ct values were (i) adjusted by centering each value around the institutional median Ct value from symptomatic children tested with that assay and (ii) converted to estimated VL (numbers of copies per milliliter) using internal or manufacturer data. Adjusted Ct values and estimated VL for asymptomatic versus symptomatic children (118 asymptomatic versus 197 symptomatic children aged 0 to 4 years, 79 asymptomatic versus 97 symptomatic children aged 5 to 9 years, 69 asymptomatic versus 75 symptomatic children aged 10 to 13 years, 73 asymptomatic versus 109 symptomatic children aged 14 to 17 years) were compared. The median adjusted Ct value for asymptomatic children was 10.3 cycles higher than for symptomatic children (P < 0.0001), and VL were 3 to 4 logs lower than for symptomatic children (P < 0.0001); differences were consistent (P < 0.0001) across all four age brackets. These differences were consistent across all institutions and by sex, ethnicity, and race. Asymptomatic children with diabetes (odds ratio [OR], 6.5; P = 0.01), a recent contact (OR, 2.3; P = 0.02), and testing for surveillance (OR, 2.7; P = 0.005) had higher estimated risks of having a Ct value in the lowest quartile than children without, while an immunocompromised status had no effect. Children with asymptomatic SARS-CoV-2 infection had lower levels of virus in their nasopharynx/oropharynx than symptomatic children, but the timing of infection relative to diagnosis likely impacted levels in asymptomatic children. Caution is recommended when choosing diagnostic tests for screening of asymptomatic children.

TNF Receptor 1 Promotes Early-Life Immunity and Protects against Colitis in Mice.

Neutralization of tumor necrosis factor (TNF) represents a widely used therapeutic strategy for autoimmune diseases including inflammatory bowel disease (IBD). However, the fact that many patients with IBD are non-responsive to anti-TNF therapies suggests the need for a better understanding of TNF signaling in IBD. Here, we show that co-deletion of TNF receptor 1 (TNFR1, Tnfrsf1a) in the Il10-/- spontaneous colitis model exacerbates disease, resulting in very-early-onset inflammation after weaning. The disease can be interrupted by treatment with antibiotics. The single deletion of TNFR1 induces subclinical colonic epithelial dysfunction and mucosal immune abnormalities, including accumulation of neutrophils and depletion of B cells. During the pre-disease period (before weaning), both Tnfr1-/- and Il10-/-Tnfr1-/- animals exhibit impaired expression of pro-inflammatory cytokines compared with wild-type and Il10-/- controls, respectively. Collectively, these results demonstrate the net anti-inflammatory functions of TNF/TNFR1 signaling through the regulation of colonic immune homeostasis in early life.

Shining a light on the pathogenicity of health care providers' mobile phones: Use of a novel ultraviolet-C wave disinfection device.

BACKGROUND: Mobile phones are known to carry pathogenic bacteria and viruses on their surfaces, posing a risk to healthcare providers (HCPs) and hospital infection prevention efforts. We utilize an Ultraviolet-C (UV-C) device to provide an effective method for mobile phone disinfection and survey HCPs about infection risk. METHODS: Environmental swabs were used to culture HCPs' personal mobile phone surfaces. Four cultures were obtained per phone: before and after the UV-C device's 30-second disinfecting cycle, at the beginning and end of a 12-hour shift. Surveys were administered to participants pre- and poststudy. RESULTS: Total bacterial colony forming units were reduced by 90.5% (P = .006) after one UV-C disinfection cycle, and by 99.9% (P = .004) after 2 cycles. Total pathogenic bacterial colony forming units were decreased by 98.2% (P = .038) after one and >99.99% (P = .037) after 2 disinfection cycles. All survey respondents were willing to use the UV-C device daily to weekly, finding it convenient and beneficial. DISCUSSION: This novel UV-C disinfecting device is effective in reducing pathogenic bacteria on mobile phones. HCPs would frequently use a phone disinfecting device to reduce infection risk. CONCLUSIONS: In light of the ongoing coronavirus (COVID-19) pandemic, a standardized approach to phone disinfection may be valuable in preventing healthcare-associated infections.

Advances in Rapid Molecular Blood Culture Diagnostics: Healthcare Impact, Laboratory Implications, and Multiplex Technologies.

BACKGROUND: For far too long, the diagnosis of bloodstream infections has relied on time-consuming blood cultures coupled with traditional organism identification and susceptibility testing. Technologies to define the culprit in bloodstream infections have gained sophistication in recent years, notably by application of molecular methods. CONTENT: In this review, we summarize the tests available to clinical laboratories for molecular rapid identification and resistance marker detection in blood culture bottles that have flagged positive. We explore the cost-benefit ratio of such assays, covering aspects that include performance characteristics, effect on patient care, and relevance to antibiotic stewardship initiatives. SUMMARY: Rapid blood culture diagnostics represent an advance in the care of patients with bloodstream infections, particularly those infected with resistant organisms. These diagnostics are relatively easy to implement and appear to have a positive cost-benefit balance, particularly when fully incorporated into a hospital's antimicrobial stewardship program.

GDH and toxin immunoassay for the diagnosis of Clostridioides (Clostridium) difficile infection is not a 'one size fit all' screening test.

Diagnosing Clostridioides (Clostridium) difficile infection is challenged by lack of a clear gold standard. We sought to determine if the two-step algorithm (screening GDH and toxin lateral flow assay followed by tcdB PCR) would have adequate clinical performance at a tertiary care center. Of 486 patients, 310 (63.8%) were immunocompromised. Of 150 PCR-positive specimens, 52 (34.7%) were toxin-positive and 126 (84.0%) were GDH positive. Positive GDH or toxin results corresponded to lower PCR cycle threshold values (P < 0.01). PCR-positive patients had more frequently documented antibiotic usage (78.4% vs 66.9%, P = 0.05) and diarrhea (91.0% vs. 79.4%, P < 0.01) and less frequent alternate etiologies of diarrhea (27.3% vs. 41.1%, P = 0.004) or laxative use (24.6% vs 36.1%, P = 0.02). Toxin positivity was associated with antibiotic use (P < 0.01), but not with neutropenia, diarrhea, malignancy, or chemotherapy (P > 0.05). The application of the 2-step algorithm should be thoroughly evaluated in immunocompromised patient populations before implementation.

Effects of Gut Bacteria Depletion and High-Na+ and Low-K+ Intake on Circulating Levels of Biogenic Amines.

SCOPE: High-sodium and low-potassium (HNaLK) content in Western diets increases the risk of hypertension and cardiovascular disease (CVD). It is investigated if the dietary minerals interact with gut bacteria to modulate circulating levels of biogenic amines, which are implicated in various pathologies, including hypertension and CVD. METHODS AND RESULTS: Using a metabolomic approach to target biogenic amines, the effects of gut bacteria depletion and HNaLK intake on circulating levels of biogenic amines in rats are examined. Forty-five metabolites whose plasma levels are significantly altered by gut bacteria depletion (p < 0.05) are found, indicating their regulation by gut bacteria. Many of them are not previously linked to gut bacteria; therefore, these data provide novel insights into physiological or pathological roles of gut bacteria. A number of plasma metabolites that are altered both by gut bacteria and HNaLK intake are also found, suggesting possible interactions of the diet and gut bacteria in the modulation of these metabolites. The diet effects are observed with significant changes in the gut bacterial taxa Porphyromonadaceae and Prevotellaceae (p < 0.05). CONCLUSION: The dietary minerals may regulate abundances of certain gut bacteria to alter circulating levels of biogenic amines, which may be linked to host physiology or pathology.

Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations.

Previous studies on the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants have provided highly variable results. Here we perform a meta-analysis of seven microbiome studies (1825 stool samples from 684 infants) to compare the gut microbiota of non-EBF and EBF infants across populations. In the first 6 months of life, gut bacterial diversity, microbiota age, relative abundances of Bacteroidetes and Firmicutes, and predicted microbial pathways related to carbohydrate metabolism are consistently higher in non-EBF than in EBF infants, whereas relative abundances of pathways related to lipid metabolism, vitamin metabolism, and detoxification are lower. Variation in predicted microbial pathways associated with non-EBF infants is larger among infants born by Caesarian section than among those vaginally delivered. Longer duration of exclusive breastfeeding is associated with reduced diarrhea-related gut microbiota dysbiosis. Furthermore, differences in gut microbiota between EBF and non-EBF infants persist after 6 months of age. Our findings elucidate some mechanisms of short and long-term benefits of exclusive breastfeeding across different populations.

Antibiotic-Resistant Bacteria and the Use of Novel Antibiotics in Children.

Infections due to antibiotic-resistant bacteria in children are on the rise worldwide. Treating these infections is a challenge for pediatric caregivers. In this arms race, the armamentarium of antibiotics is quickly being depleted. This article reviews the problems facing clinicians caring for children with resistant bacterial infections, examines some of the newer antibiotics, and discusses other methods for pediatric caregivers to combat these infections. Only through an informed and concerted effort will we be able to address this growing problem in children. [Pediatr Ann. 2018;47(9):e354-e358.].

Quantification of variation and the impact of biomass in targeted 16S rRNA gene sequencing studies.

BACKGROUND: Recent advances in sequencing technologies and bioinformatics tools have allowed for large-scale microbiome studies that are rapidly advancing medical research. However, small changes in technique or analysis can significantly alter the results and lead to conflicting findings. Quantifying the technical versus biological variation expected in targeted 16S rRNA gene sequencing studies and how this variation changes with input biomass is critical to guide meaningful interpretation of the current literature and plan future research. RESULTS: Data were compiled from 469 sequencing libraries across 19 separate targeted 16S rRNA gene sequencing runs over a 2.5-year time period. Following removal of contaminant sequences identified from negative controls, 244 samples retained sufficient reads for further analysis. Coefficients of variation for intra- and inter-assay variation from repeated measurements of a bacterial mock community ranged from 8.7 to 37.6% (intra) and 15.6 to 80.5% (inter) for all but one genus of bacteria whose relative abundance was greater than 1%. Intra- versus inter-assay Bray-Curtis pairwise distances for a single stool sample were 0.11 versus 0.31, whereas intra-assay variation from repeat stool samples from the same donor was greater at 0.38 (Wilcoxon p = 0.001). A dilution series of the bacterial mock community was used to assess the effect of input biomass on variability. Pairwise distances increased with more dilute samples, and estimates of relative abundance became unreliable below approximately 100 copies of the 16S rRNA gene per microliter. Using this data, we created a prediction model to estimate the expected variation in microbiome measurements for given input biomass and relative abundance values. CONCLUSIONS: Well-controlled microbiome studies are sufficiently robust to capture small biological effects and can achieve levels of variability consistent with clinical assays. Relative abundance is negatively associated with measures of variability and has a stronger effect on variability than does absolute biomass, suggesting that it is feasible to detect differences in bacterial populations in very low-biomass samples. Further, by quantifying the effect of biomass and relative abundance on compositional variability, we developed a tool for defining the expected variance in a given microbiome study.