Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC
ABSTRACT Mpox is an emerging zoonotic disease that caused two public health emergencies of international concern within two years. Less is known about the interplay of microbial organisms in mpox lesions which could result in superinfections that exacerbate outcomes or delay recovery. We utilized a...
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American Society for Microbiology
2025-07-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.00512-25 |
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| author | Leonard Schuele Leandre Murhula Masirika Hayley Cassidy Philip T. L. C. Clausen Luca M. Zaeck Marjan Boter Pacifique Ndishimye Jean Claude Udahemuka Rory D. de Vries Saria Otani Richard Molenkamp David F. Nieuwenhuijse Justin Bengehya Mbiribindi Freddy Belesi Siangoli Marion Koopmans Frank M. Aarestrup Bas B. Oude Munnink |
| author_facet | Leonard Schuele Leandre Murhula Masirika Hayley Cassidy Philip T. L. C. Clausen Luca M. Zaeck Marjan Boter Pacifique Ndishimye Jean Claude Udahemuka Rory D. de Vries Saria Otani Richard Molenkamp David F. Nieuwenhuijse Justin Bengehya Mbiribindi Freddy Belesi Siangoli Marion Koopmans Frank M. Aarestrup Bas B. Oude Munnink |
| author_sort | Leonard Schuele |
| collection | DOAJ |
| description | ABSTRACT Mpox is an emerging zoonotic disease that caused two public health emergencies of international concern within two years. Less is known about the interplay of microbial organisms in mpox lesions which could result in superinfections that exacerbate outcomes or delay recovery. We utilized a unified metagenomic sequencing approach involving slow-speed centrifugation and differential lysis on 19 mpox lesion swabs of hospitalized patients in South Kivu province (eastern DRC) to characterize bacteria, antimicrobial resistance genes, mpox virus (MPXV), and viral co-infections. High-quality MPXV whole-genome sequences were obtained until a Ct value of 27. Furthermore, co-infections with other clinically relevant viruses, such as varicella zoster virus and herpes simplex virus-2, were detected and confirmed by real-time PCR. In addition, metagenomic sequence analysis of the bacterial content showed the presence of bacteria associated with skin and soft tissue infection in 10 of the 19 samples analyzed. These bacteria had a high abundance of resistance genes, with possible implications for antimicrobial treatment based on the predicted antimicrobial resistance. In conclusion, we report the presence of bacterial and viral pathogens in mpox lesions and detection of widespread resistance genes to the standard antibiotic treatment. The possibility of a co-infection, including antimicrobial resistance, should be considered when discussing treatment options, along with the determination of the case-fatality ratio.IMPORTANCEThe mpox virus clade Ib lineage emerged in the eastern Democratic Republic of the Congo owing to continuous human-to-human transmission in a vulnerable patient population. A major challenge of this ongoing outbreak is its occurrence in regions with severely limited healthcare infrastructure. As a result, less is known about co-infections in affected patients. Identifying and characterizing pathogens, including their antimicrobial resistance, is crucial for reducing infection-related complications and improving antimicrobial stewardship. In this study, we applied a unified metagenomics approach to detect and characterize bacterial and viral co-infections in mpox lesions of hospitalized mpox patients in the eastern DRC. |
| format | Article |
| id | doaj-art-dea5326effee4c7999d56e53b3eb84c2 |
| institution | DOAJ |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | American Society for Microbiology |
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| series | Microbiology Spectrum |
| spelling | doaj-art-dea5326effee4c7999d56e53b3eb84c22025-08-20T03:14:57ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-07-0113710.1128/spectrum.00512-25Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRCLeonard Schuele0Leandre Murhula Masirika1Hayley Cassidy2Philip T. L. C. Clausen3Luca M. Zaeck4Marjan Boter5Pacifique Ndishimye6Jean Claude Udahemuka7Rory D. de Vries8Saria Otani9Richard Molenkamp10David F. Nieuwenhuijse11Justin Bengehya Mbiribindi12Freddy Belesi Siangoli13Marion Koopmans14Frank M. Aarestrup15Bas B. Oude Munnink16Department of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsCentre de Recherche en Sciences Naturelles de Lwiro, South-Kivu, Bukavu, Democratic Republic of the CongoDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, DenmarkDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsCongo Outbreaks, Research for Development (CORD), South-Kivu, Bukavu, Democratic Republic of the CongoCongo Outbreaks, Research for Development (CORD), South-Kivu, Bukavu, Democratic Republic of the CongoDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, DenmarkDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsCongo Outbreaks, Research for Development (CORD), South-Kivu, Bukavu, Democratic Republic of the CongoCongo Outbreaks, Research for Development (CORD), South-Kivu, Bukavu, Democratic Republic of the CongoDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsResearch Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, DenmarkDepartment of Viroscience, Erasmus University Medical Center, Rotterdam, the NetherlandsABSTRACT Mpox is an emerging zoonotic disease that caused two public health emergencies of international concern within two years. Less is known about the interplay of microbial organisms in mpox lesions which could result in superinfections that exacerbate outcomes or delay recovery. We utilized a unified metagenomic sequencing approach involving slow-speed centrifugation and differential lysis on 19 mpox lesion swabs of hospitalized patients in South Kivu province (eastern DRC) to characterize bacteria, antimicrobial resistance genes, mpox virus (MPXV), and viral co-infections. High-quality MPXV whole-genome sequences were obtained until a Ct value of 27. Furthermore, co-infections with other clinically relevant viruses, such as varicella zoster virus and herpes simplex virus-2, were detected and confirmed by real-time PCR. In addition, metagenomic sequence analysis of the bacterial content showed the presence of bacteria associated with skin and soft tissue infection in 10 of the 19 samples analyzed. These bacteria had a high abundance of resistance genes, with possible implications for antimicrobial treatment based on the predicted antimicrobial resistance. In conclusion, we report the presence of bacterial and viral pathogens in mpox lesions and detection of widespread resistance genes to the standard antibiotic treatment. The possibility of a co-infection, including antimicrobial resistance, should be considered when discussing treatment options, along with the determination of the case-fatality ratio.IMPORTANCEThe mpox virus clade Ib lineage emerged in the eastern Democratic Republic of the Congo owing to continuous human-to-human transmission in a vulnerable patient population. A major challenge of this ongoing outbreak is its occurrence in regions with severely limited healthcare infrastructure. As a result, less is known about co-infections in affected patients. Identifying and characterizing pathogens, including their antimicrobial resistance, is crucial for reducing infection-related complications and improving antimicrobial stewardship. In this study, we applied a unified metagenomics approach to detect and characterize bacterial and viral co-infections in mpox lesions of hospitalized mpox patients in the eastern DRC.https://journals.asm.org/doi/10.1128/spectrum.00512-25mpoxmpox virusclade Ibmetagenomicsantimicrobial resistanceco-infections |
| spellingShingle | Leonard Schuele Leandre Murhula Masirika Hayley Cassidy Philip T. L. C. Clausen Luca M. Zaeck Marjan Boter Pacifique Ndishimye Jean Claude Udahemuka Rory D. de Vries Saria Otani Richard Molenkamp David F. Nieuwenhuijse Justin Bengehya Mbiribindi Freddy Belesi Siangoli Marion Koopmans Frank M. Aarestrup Bas B. Oude Munnink Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC Microbiology Spectrum mpox mpox virus clade Ib metagenomics antimicrobial resistance co-infections |
| title | Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC |
| title_full | Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC |
| title_fullStr | Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC |
| title_full_unstemmed | Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC |
| title_short | Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC |
| title_sort | metagenomic sequencing of mpox virus clade ib lesions identifies possible bacterial and viral co infections in hospitalized patients in eastern drc |
| topic | mpox mpox virus clade Ib metagenomics antimicrobial resistance co-infections |
| url | https://journals.asm.org/doi/10.1128/spectrum.00512-25 |
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