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Yek C, Lay S, Chea S, Bohl J, Oum M, Ly S, Sath R, Ahyong V, Tato C, Seng H, Ly S, Lon C, Manning J. 1176. Metagenomic Next-Generation Sequencing of Nasopharyngeal Swabs in Acute Febrile Illness in Cambodia. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.1013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
There is growing recognition of metagenomic next-generation sequencing (mNGS) as a valuable diagnostic tool capable of providing unbiased pathogen detection, but data on performance in low-resource settings remains scant. Here, we use mNGS of nasopharyngeal (NP) swabs taken from subjects in Cambodia to identify potential pathogens causing acute febrile illness.
Methods
Febrile subjects aged 2 months to 65 years were enrolled in a cross-sectional study conducted across 4 tertiary hospitals in Cambodia. NP swabs were collected at hospital presentation. Depending on reported symptom constellations, sera was also taken in a subset of subjects for comparison of mNGS results. RNA was isolated from biosamples, converted to cDNA libraries, and sequenced on a NextSeq2000 (Illumina). Raw sequence reads were stripped for host reads and aligned to NCBI nucleotide and protein databases using a cloud-based bioinformatics platform (CZID).
Results
NP swabs were collected from 97 subjects between April 2020 and June 2021. Subjects were predominantly male (53.6%) and young (median age 3 years [IQR 1-25]). Pathogens were identified in 42 (43.2%) NP swabs; of these, 26 (61.9%) were respiratory viruses including 9 rhinovirus, 7 coronavirus (1 SARS-CoV-2), and 5 respirovirus cases. Co-infection was identified in 3 subjects with coronavirus and respirovirus (N=2) and coronavirus and rhinovirus (N=1). Of subjects with paired sera and NP samples (N=61), 18 (29.5%) had positive NP swabs but negative sera, 7 (11.5%) had negative NP swabs but positive sera, 12 (19.7%) had positive NP swabs and sera, and 24 (39.3%) had negative NP swabs and sera. Pathogen hits correlated in NP swabs and sera in 10 of 12 subjects, including six subjects with chikungunya.
Conclusion
mNGS can be successfully implemented in low-resource settings to identify emerging pathogens and common respiratory pathogens, including co-infecting pathogens, from NP swabs of febrile patients. mNGS may also be able to detect chikungunya from NP swab alone, raising the possibility of non-invasive diagnostics for infections associated with high viremic states.
Disclosures
All Authors: No reported disclosures.
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Affiliation(s)
- Christina Yek
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
| | - Sreyngim Lay
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
| | - Sophana Chea
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
| | - Jennifer Bohl
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
| | - Mengheng Oum
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
| | - Sokna Ly
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
| | - Ratanak Sath
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
| | - Vida Ahyong
- Chan Zuckerberg Biohub , San Francisco, California
| | | | - Heng Seng
- Ministry of Health , Phnom Penh, Phnom Penh , Cambodia
| | - Sovann Ly
- Ministry of Health , Phnom Penh, Phnom Penh , Cambodia
| | - Chanthap Lon
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
| | - Jessica Manning
- National Institute of Allergy and Infectious Diseases , Bethesda, Maryland
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