tetano
Editor, Senior Moderator
Infect Control Hosp Epidemiol
. 2025 Nov 4:1-11.
doi: 10.1017/ice.2025.10328. Online ahead of print. Genomic epidemiology of healthcare-associated respiratory virus infections in Pittsburgh, Pennsylvania, 2018-2020
Vatsala Rangachar Srinivasa[SUP] 1 2 3 [/SUP], Marissa P Griffith[SUP] 1 2 [/SUP], Alexander J Sundermann[SUP] 1 3 [/SUP], Emma Mills[SUP] 2 [/SUP], Nathan J Raabe[SUP] 1 2 3 [/SUP], Kady D Waggle[SUP] 1 2 [/SUP], Kathleen A Shutt[SUP] 1 2 [/SUP], Tung Phan[SUP] 4 [/SUP], Anna F Wang-Erickson[SUP] 3 5 6 [/SUP], Graham M Snyder[SUP] 2 7 [/SUP], Daria Van Tyne[SUP] 2 [/SUP], Lora Lee Pless[SUP] #[/SUP][SUP] 1 2 [/SUP], Lee H Harrison[SUP] #[/SUP][SUP] 1 2 3 [/SUP]
Affiliations
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 three teaching hospitals.
Methods: From January 2, 2018, to January 4, 2020, nasal swab specimens positive for rhinovirus, influenza virus, human metapneumovirus (HMPV), or respiratory syncytial virus (RSV) from patients hospitalized for ≥3 days were sequenced. High-quality genomes were assessed for genetic relatedness using ≤3 single nucleotide polymorphisms (SNPs) as a cutoff, 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 virus (n = 50), RSV (n = 48), and HMPV (n = 47). Of these, 42%% (152/359 patients) were from a pediatric hospital, and 58% were from adult hospitals. WGS was performed on 61.2% (178/291) rhinovirus, 78% (39/50) influenza virus, 90% (43/48) RSV, and all HMPV specimens. Among high-quality genomes, we identified 14 genetically related clusters involving 36 patients (range: 2-5 patients per cluster). We identified common epidemiological links for 53% (19/36) of clustered patients; 63% (12/19) of patients had same-unit stays, 26% (5/19) had overlapping hospital stays, and 11% (2/19) shared common providers. On average, genetically related clusters spanned 16 days (range: 0 - 55 days).
Conclusion: WGS offered new insights into respiratory virus transmission dynamics. These advancements could potentially improve infection prevention and control strategies, leading to enhanced patient safety and healthcare outcomes.
. 2025 Nov 4:1-11.
doi: 10.1017/ice.2025.10328. Online ahead of print. Genomic epidemiology of healthcare-associated respiratory virus infections in Pittsburgh, Pennsylvania, 2018-2020
Vatsala Rangachar Srinivasa[SUP] 1 2 3 [/SUP], Marissa P Griffith[SUP] 1 2 [/SUP], Alexander J Sundermann[SUP] 1 3 [/SUP], Emma Mills[SUP] 2 [/SUP], Nathan J Raabe[SUP] 1 2 3 [/SUP], Kady D Waggle[SUP] 1 2 [/SUP], Kathleen A Shutt[SUP] 1 2 [/SUP], Tung Phan[SUP] 4 [/SUP], Anna F Wang-Erickson[SUP] 3 5 6 [/SUP], Graham M Snyder[SUP] 2 7 [/SUP], Daria Van Tyne[SUP] 2 [/SUP], Lora Lee Pless[SUP] #[/SUP][SUP] 1 2 [/SUP], Lee H Harrison[SUP] #[/SUP][SUP] 1 2 3 [/SUP]
Affiliations
- PMID: 41185586
- DOI: 10.1017/ice.2025.10328
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 three teaching hospitals.
Methods: From January 2, 2018, to January 4, 2020, nasal swab specimens positive for rhinovirus, influenza virus, human metapneumovirus (HMPV), or respiratory syncytial virus (RSV) from patients hospitalized for ≥3 days were sequenced. High-quality genomes were assessed for genetic relatedness using ≤3 single nucleotide polymorphisms (SNPs) as a cutoff, 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 virus (n = 50), RSV (n = 48), and HMPV (n = 47). Of these, 42%% (152/359 patients) were from a pediatric hospital, and 58% were from adult hospitals. WGS was performed on 61.2% (178/291) rhinovirus, 78% (39/50) influenza virus, 90% (43/48) RSV, and all HMPV specimens. Among high-quality genomes, we identified 14 genetically related clusters involving 36 patients (range: 2-5 patients per cluster). We identified common epidemiological links for 53% (19/36) of clustered patients; 63% (12/19) of patients had same-unit stays, 26% (5/19) had overlapping hospital stays, and 11% (2/19) shared common providers. On average, genetically related clusters spanned 16 days (range: 0 - 55 days).
Conclusion: WGS offered new insights into respiratory virus transmission dynamics. These advancements could potentially improve infection prevention and control strategies, leading to enhanced patient safety and healthcare outcomes.