Shotgun metagenomic characterization of human adenovirus F40 and a non-cpe Clostridium perfringens strain in pediatric prolonged diarrhea: a genome-resolved case study
4 affiliations
- 1Faculty of Science, Suez Canal University, Ismailia, Egypt
- 2Faculty of Pharmacy, Al-Farahidi University, Baghdad, Iraq
- 3Biotechnology Research Institute, Suez Canal University, Ismailia, Egypt
- 4EmbryoCo, Health Sciences Research Center, Princess Nourah Bint Abdulrahman University, Riyadh, 13412 Saudi Arabia
Abstract
Background: Viral and bacterial pathogens may be concurrently detected in pediatric gastroenteritis, yet such findings are often missed by routine diagnostic methods. Shotgun metagenomic sequencing enables comprehensive detection and genomic characterization of microorganisms present in clinical specimens, including pathogens that may not be recovered by conventional testing.
Methods: Shotgun metagenomic sequencing was performed on a single pediatric diarrheic stool sample, followed by quality filtering, de novo assembly, taxonomic classification, phylogenetic reconstruction, and integrated virulome-resistome profiling, including plasmid-associated resistance elements.
Results: Routine diagnostics identified adenovirus as the sole pathogen. Metagenomic analysis confirmed human adenovirus F40 (HAdV-F40), showing close phylogenetic relatedness to globally distributed HAdV-F40 reference strains and a clear distinction from HAdV-F41. In addition, metagenomics uniquely detected a Clostridium perfringens strain (SAM_A8, ST-5) that was not recovered by culture. The strain lacked the classical enterotoxin gene (cpe) but harbored a conserved histotoxic virulence profile, including cpa, pfoA, colA, hyaluronidases, and sialidases. Plasmid-associated tetracycline resistance genes (tetA(P) and tetB(P)) were also identified.
Conclusion: This case study demonstrates the feasibility of shotgun metagenomic sequencing for comprehensive detection and genomic characterization of microorganisms present in pediatric diarrheal stool specimens, including organisms not identified by routine diagnostics. The findings are descriptive and highlight the value of metagenomics as a complementary diagnostic approach. However, no conclusions regarding pathogenic synergy, causality, or the clinical contribution of the co-detected organisms can be drawn from this single case.
Supplementary information: The online version contains supplementary material available at https://doi.org/10.1186/s12879-026-14694-5.
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BibTeX
@article{elshahidy2026shotgun,
title = {{Shotgun metagenomic characterization of human adenovirus F40 and a non-cpe Clostridium perfringens strain in pediatric prolonged diarrhea: a genome-resolved case study}},
author = {Samar M. El-Shahidy and Amira M. Zakaria and Mohanad A. Ibrahim and Atef M. Diab},
journal = {BMC Infectious Diseases},
year = {2026},
month = nov,
doi = {10.1186/s12879-026-14694-5},
url = {https://doi.org/10.1186/s12879-026-14694-5},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Shotgun metagenomic characterization of human adenovirus F40 and a non-cpe Clostridium perfringens strain in pediatric prolonged diarrhea: a genome-resolved case study
AU - Samar M. El-Shahidy
AU - Amira M. Zakaria
AU - Mohanad A. Ibrahim
AU - Atef M. Diab
PY - 2026
DA - 2026/11/03
JO - BMC Infectious Diseases
DO - 10.1186/s12879-026-14694-5
UR - https://doi.org/10.1186/s12879-026-14694-5
AB - Background: Viral and bacterial pathogens may be concurrently detected in pediatric gastroenteritis, yet such findings are often missed by routine diagnostic methods. Shotgun metagenomic sequencing enables comprehensive detection and genomic characterization of microorganisms present in clinical specimens, including pathogens that may not be recovered by conventional testing. Methods: Shotgun metagenomic sequencing was performed on a single pediatric diarrheic stool sample, followed by quality filtering, de novo assembly, taxonomic classification, phylogenetic reconstruction, and integrated virulome-resistome profiling, including plasmid-associated resistance elements. Results: Routine diagnostics identified adenovirus as the sole pathogen. Metagenomic analysis confirmed human adenovirus F40 (HAdV-F40), showing close phylogenetic relatedness to globally distributed HAdV-F40 reference strains and a clear distinction from HAdV-F41. In addition, metagenomics uniquely detected a Clostridium perfringens strain (SAM_A8, ST-5) that was not recovered by culture. The strain lacked the classical enterotoxin gene (cpe) but harbored a conserved histotoxic virulence profile, including cpa, pfoA, colA, hyaluronidases, and sialidases. Plasmid-associated tetracycline resistance genes (tetA(P) and tetB(P)) were also identified. Conclusion: This case study demonstrates the feasibility of shotgun metagenomic sequencing for comprehensive detection and genomic characterization of microorganisms present in pediatric diarrheal stool specimens, including organisms not identified by routine diagnostics. The findings are descriptive and highlight the value of metagenomics as a complementary diagnostic approach. However, no conclusions regarding pathogenic synergy, causality, or the clinical contribution of the co-detected organisms can be drawn from this single case. Supplementary information: The online version contains supplementary material available at https://doi.org/10.1186/s12879-026-14694-5.
SN - 1471-2334
ER -