Shotgun metagenomic characterization of human adenovirus F40 and a non-cpe Clostridium perfringens strain in pediatric prolonged diarrhea: a genome-resolved case study.
Samar M El-Shahidy, Amira M Zakaria, Mohanad A Ibrahim et al.
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Case in brief
A child with prolonged diarrhea had adenovirus identified as the sole pathogen by routine testing. Shotgun metagenomic sequencing of stool confirmed human adenovirus F40 (HAdV-F40), phylogenetically distinct from HAdV-F41, and also detected a Clostridium perfringens strain (SAM_A8, ST-5) that culture had not recovered. The strain lacked the classical enterotoxin gene cpe but carried histotoxic virulence genes and plasmid-associated tetracycline resistance genes tetA(P) and tetB(P). The report provides genomic characterization of both organisms; it does not establish whether either, or their co-detection, caused or contributed to the prolonged diarrhea.
What made this case unusual
Metagenomics detected a culture-negative C. perfringens strain lacking cpe but carrying a histotoxic virulence profile, alongside HAdV-F40. The clinical significance of this co-detection remains undetermined.
Diagnostic / clinical pearl
A negative culture does not exclude detection of a microorganism by shotgun metagenomics, but genomic detection alone does not establish its clinical contribution.
Why it matters
The case illustrates how metagenomic sequencing can complement routine diagnostics by identifying and characterizing organisms missed by conventional testing.