Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens.

The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive-requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively, P = 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively. IMPORTANCE: To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.

Clinical utility of SARS-CoV-2 subgenomic RT-PCR in a pediatric quaternary care setting.

BACKGROUND: During active transcription, SARS-CoV-2 generates subgenomic regions of viral RNA. While standard SARS-CoV-2 RT-PCR amplifies region(s) of genomic RNA, it cannot distinguish active infection from remnant viral genomic material. However, screening for subgenomic RNA (sgRNA) by RT-PCR may aid in the determination of actively transcribing virus. OBJECTIVES: To evaluate the clinical utility of SARS-CoV-2 sgRNA RT-PCR testing in a pediatric population. STUDY DESIGN: Retrospective analysis was performed on inpatients from February-September 2022 positive for SARS-CoV-2 by RT-PCR with a concomitant order for sgRNA RT-PCR. Chart abstractions were conducted to determine clinical outcomes, management, and infection prevention and control (IPC) practices. RESULTS: Of 95 SARS-CoV-2 positive samples from 75 unique patients, 27 (28.4%) were positive by sgRNA RT-PCR. A negative sgRNA RT-PCR test allowed for de-isolation in 68 (71.6%) patient episodes. Regardless of age or sex, a positive sgRNA RT-PCR result significantly correlated with disease severity (P = 0.007), generalized COVID-19 symptoms (P = 0.012), hospitalization for COVID-19 (P = 0.019), and immune status (P = 0.024). Moreover, sgRNA RT-PCR results prompted changes in management in 28 patients (37.3%); specifically, therapeutic escalation in 13/27 (48.1%) positives and de-escalation in 15/68 (22.1%) negatives. CONCLUSIONS: Taken together, these findings underscore the clinical utility of sgRNA RT-PCR testing in a pediatric population as we report significant associations between sgRNA RT-PCR results and clinical parameters related to COVID-19. These findings align with the proposed use of sgRNA RT-PCR testing to guide patient management and IPC practices in the hospital setting.

Parent Perceptions of a Validated Asthma Questionnaire in the Emergency Department.

OBJECTIVE: While a number asthma questionnaires have been validated, most have not been used in an emergency department (ED) setting, nor evaluated patient feedback or clinical benefit. We sought to evaluate parent feedback on an asthma questionnaire used in an ED setting. METHODS: We recruited parents of children 2-17 years old presenting to a tertiary pediatric ED for asthma care. Parents first completed then rated the Pediatric Asthma Control and Communication Instrument (PACCI-ED). RESULTS: One hundred seventy-four parents (84%) completed surveys. Approximately two-thirds were Latinx, and 82% completed high school. Ninety-three percent of children had uncontrolled asthma. Parents endorsed the PACCI-ED: as easy to answer (94%); useful in understanding their child's asthma (83%); used the right words to describe their child's condition (95%); and would help the ED physician (93%) and primary care provider (PCP) (89%) better understand their child's asthma. Eleven percent reported that the PACCI-ED interfered with ED care. Parents with lower health literacy were more likely to agree the PACCI-ED asked more complete questions about their child's asthma than the ED physician (64% vs 45%, P = .02). Parents of children with uncontrolled asthma were more likely to agree that the PACCI-ED should become part of regular ED care (88% vs 62%, P = .02). Parents were more likely to agree that the PACCI-ED would help their PCP understand their child's asthma if they had a lower income (92% vs 50%, P < .001), less education (100% vs 88%, P = .004), were Latinx (94% vs 83%, P = .006), or were not using controller medication (93% vs 83%, P = .03). CONCLUSIONS: Parents endorse an asthma questionnaire as valuable during an ED encounter. Because it is endorsed to be valuable to parents, this questionnaire could be used to facilitate patient-centered asthma care.

Complex Care Hospital Use and Postdischarge Coaching: A Randomized Controlled Trial.

OBJECTIVES: We sought to examine the effect of a caregiver coaching intervention, Plans for Action and Care Transitions (PACT), on hospital use among children with medical complexity (CMC) within a complex care medical home at an urban tertiary medical center. METHODS: PACT was an 18-month caregiver coaching intervention designed to influence key drivers of hospitalizations: (1) recognizing critical symptoms and conducting crisis plans and (2) supporting comprehensive hospital transitions. Usual care was within a complex care medical home. Primary outcomes included hospitalizations and 30-day readmissions. Secondary outcomes included total charges and mortality. Intervention effects were examined with bivariate and multivariate analyses. RESULTS: From December 2014 to September 2016, 147 English- and Spanish-speaking CMC <18 years old and their caregivers were randomly assigned to PACT (n = 77) or usual care (n = 70). Most patients were Hispanic, Spanish-speaking, and publicly insured. Although in unadjusted intent-to-treat analyses, only charges were significantly reduced, both hospitalizations and charges were lower in adjusted analyses. Hospitalization rates (per 100 child-years) were 81 for PACT vs 101 for usual care (adjusted incident rate ratio: 0.61 [95% confidence interval 0.38-0.97]). Adjusted mean charges per patient were $14 206 lower in PACT. There were 0 deaths in PACT vs 4 in usual care (log-rank P = .04). CONCLUSIONS: Among CMC within a complex care program, a health coaching intervention designed to identify, prevent, and manage patient-specific crises and postdischarge transitions appears to lower hospitalizations and charges. Future research should confirm findings in broader populations and care models.