Multiple Respiratory Syncytial Virus Introductions Into a Neonatal Intensive Care Unit

Genomic Epidemiology of Healthcare-Associated Respiratory Virus Infections

Background

Respiratory virus transmission in healthcare settings is not well understood. To investigate the transmission dynamics of common healthcare-associated respiratory virus infections, we performed retrospective whole genome sequencing (WGS) surveillance at one pediatric and two adult teaching hospitals in Pittsburgh, PA.

Methods

From January 2, 2018, to January 4, 2020, nasal swab specimens positive for rhinovirus, influenza, human metapneumovirus (HMPV), or respiratory syncytial virus (RSV) from patients hospitalized for ≥3 days were sequenced on Illumina platform. High-quality genomes were assessed for genetic relatedness using ≤3 single nucleotide polymorphisms (SNPs) cut-off, except for rhinovirus (10 SNPs). Patient health records were reviewed for genetically related clusters to identify epidemiological connections.

Results

We collected 436 viral specimens from 359 patients: rhinovirus (n=291), influenza (n=50), HMPV (n=47), and RSV (n=48). Of these, 55% (197/359 patients) were from pediatric hospital and 45% from adult hospitals. Patients ranged in age from 14 days to 93 years, 61% were male, and 74% were white. WGS was performed on 61.2% (178/291) rhinovirus, 78% (39/50) influenza, 92% (44/48) RSV, and all HMPV specimens. Among high-quality genomes, we identified 14 genetically related clusters involving 36 patients, ranging in size from 2-5 patients. We identified common epidemiological links for 53% (19/36) of clustered patients; 63% (12/19) patients had same-unit stay, 26% (5/19) had overlapping hospital stays, and 11% (2/19) shared common provider. On average, genetically related clusters spanned 16 days (range:0-55 days).

Conclusion

WGS offered insights into respiratory virus transmission dynamics. These advancements could potentially improve infection prevention and control strategies, leading to enhanced patient safety and healthcare outcomes.

Summary

We performed retrospective whole genome sequencing surveillance of common healthcare-associated respiratory virus infections across three hospitals. Our investigation elucidated complex respiratory virus transmission dynamics, which could potentially improve infection prevention and control strategies, leading to enhanced patient safety and healthcare outcomes.

SHEA NICU white paper series: Practical approaches for the prevention of viral respiratory infections

This white paper provides clinicians and hospital leaders with practical guidance on the prevention and control of viral respiratory infections in the neonatal intensive care unit (NICU). This document serves as a companion to Centers for Disease Control and Prevention Healthcare Infection Control Practices Advisory Committee (HICPAC)'s "Prophylaxis and Screening for Prevention of Viral Respiratory Infections in Neonatal Intensive Care Unit Patients: A Systematic Review." It provides practical, expert opinion and/or evidence-based answers to frequently asked questions about viral respiratory detection and prevention in the NICU. It was developed by a writing panel of pediatric and pathogen-specific experts who collaborated with members of the HICPAC systematic review writing panel and the SHEA Pediatric Leadership Council to identify questions that should be addressed. The document has been endorsed by SHEA, the American Hospital Association (AHA), The Joint Commission, the Pediatric Infectious Diseases Society (PIDS), the Association for Professionals in Infection Control and Epidemiology (APIC), the Infectious Diseases Society of America (IDSA), and the National Association of Neonatal Nurses (NANN).

Respiratory syncytial virus nosocomial outbreak in neonatal intensive care: A review of the incidence, management, and outcomes

BACKGROUND

The main objective was to determine the incidence, management, and outcomes of respiratory syncytial virus nosocomial infection (RSVNI) outbreaks in neonatal intensive care units.

METHODS

A comprehensive search of RSVNI in 9 databases was conducted from January 1, 2000 to May 1, 2021, of which the Cochrane Library comprised the Cochrane central register of controlled trials and the Cochrane database of systematic reviews. Two hundred and twenty-eight articles were retrieved and 17 were retained. A descriptive analysis was performed, and frequencies are reported as mean, median, and range where pertinent.

RESULTS

One hundred and seventeen infants were analyzed and comprised preterms (88.1%) and those with pre-existing co-morbidities. The estimated proportional incidence of RSVNI was 23.8% (177/744) infants. Outbreaks were principally managed by conventional protective measures, neonatal intensive care unit closure, and visitor restriction. Palivizumab was used to control RSVNI in 10 studies. RSVNI-related mortality was 8.5% (15/177) and 8.0% (7/87) among infants where infection control was solely employed.

CONCLUSION

RSVNI is associated with significant morbidity and mortality. The use of palivizumab should be a multidisciplinary decision, based on rapidly spreading infection. Prospective studies are essential to determine the cost-benefit of palivizumab versus standard prevention control for an RSVNI outbreak.

Next-generation sequencing of human respiratory syncytial virus subgroups A and B genomes

Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Whole genome sequencing of HRSV offers enhanced resolution of strain variability for epidemiological surveillance and provides genomic information essential for antiviral and vaccine development. A 10-amplicon one-step RT-PCR assay and a 20-amplicon nested RT-PCR assay with enhanced sensitivity were developed to amplify whole HRSV genomes from samples containing high and low viral loads, respectively. Ninety-six HRSV-positive samples comprised of 58 clinical specimens and 38 virus isolates with C_t values ≤ 24 were amplified successfully using the 10-amplicon one-step RT-PCR method and multiplexed in a single MiSeq run. Genome coverage exceeded 99.3% for all 96 samples. The 20-amplicon nested RT-PCR NGS method was used to generate >99.6% HRSV full-length genome for 72 clinical specimens with C_t values ranging from 24 to 33. Phylogenetic analysis of the genome sequences obtained from the 130 clinical specimens revealed a wide diversity of HRSV genotypes demonstrating methodologic robustness.