Genomic epidemiology of invasive Staphylococcus aureus in southwestern Nigeria

Abstract Background Staphylococcus aureus is a leading cause of hospital and community-associated human infections. Despite its clinical importance, molecular epidemiology data in Nigeria are limited. This study characterized bloodstream S. aureus isolates submitted to the Nigerian Antimicrobial Resistance Surveillance System. Methods Bloodstream S. aureus isolates from six tertiary healthcare institutions in Nigeria collected between 2016 and 2021 were characterized by antimicrobial susceptibility testing and whole-genome sequencing. Bioinformatic analyses were conducted using publicly available pipelines in addition to contextualization with publicly available sequences. Results Of 138 isolates, 85 (61.6%) were methicillin-resistant S. aureus (MRSA). A total of 31 spa types, 14 sequence types (STs), eight clonal complexes (CCs) - CC1, CC5, CC8, CC15, CC30, CC45, CC88, CC121 - and two singletons (ST152 and ST11258) were identified. ST152 (n = 48, 35%) was the predominant lineage, followed by ST772 (n = 21, 15%), ST8 (n = 16, 12%) and ST789 (n = 13, 9%). These lineages were detected across sentinel sites, indicating widespread geographic dissemination. ST772-MRSA isolates possessed the highest number of antimicrobial (AMR) and virulence genes. ST789 was characterized by numerous AMR genes in both MRSA and MSSA backgrounds, whereas ST8 and ST152-MRSA isolates demonstrated abundant virulence genes, with comparatively few AMR genes. ST152, ST772, and ST789 genomes generally clustered together relative to publicly available genomes of the corresponding STs, with lineage-specific subclades differentiated by AMR profiles. Conclusion Predominance of ST152-MRSA, ST772-MRSA, and ST789-MRSA among bloodstream S. aureus isolates in Nigeria is a significant public health concern. Sustained genomic surveillance is critical to inform infection prevention and control in Nigeria.

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Journal
Research Square
Published
2026-11-10
DOI
https://doi.org/10.21203/rs.3.rs-11363950/v1
Primary Topic
Antimicrobial Resistance in Staphylococcus
Type
preprint
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preprint

Genomic epidemiology of invasive Staphylococcus aureus in southwestern Nigeria

Oyinlola O. Oduyebo, Silvia Argimón, Abayomi Fadeyi, RA Raheem et al.
Research Square
Antimicrobial Resistance in Staphylococcus
preprint

Genomic epidemiology of invasive Staphylococcus aureus in southwestern Nigeria

Oyinlola O. Oduyebo, Silvia Argimón, Abayomi Fadeyi, RA Raheem, Ifeoluwa Komolafe, Mihir Kekre, Victoria A. Aikhomu, Odion O. Ikhimiukor, Gabriel Temitope Sunmonu, Erkison Ewomazino Odih, Iruka N. Okeke, Olatunde F Olabisi, Oyekola V. Abiri, Charles John Elikwu, Anthony P. Underwood, Veronica Olatimbo Ogunleye, Bashirat Ayobola Olanipekun, Abiodun Jumoke Egwuenu, Tochi Joy Okwor, Aaron Oladipo Aboderin, Josephine Folashade Ojo, Ayorinde O. Afolayan, David M. Aanensen, Temitope O Obadare, Anderson O. Oaikhena, Aderemi Oludiran Kehinde, Adebayo Osagie Shittu, Dorothy Cyril‐Okoh, Ihekweazu Chikwe, Adewale A Amupitan, Philip O. Oshun, Ifeanyi E. Mba, Abolaji T. Adeyemo
preprint en

Abstract

Abstract Background Staphylococcus aureus is a leading cause of hospital and community-associated human infections. Despite its clinical importance, molecular epidemiology data in Nigeria are limited. This study characterized bloodstream S. aureus isolates submitted to the Nigerian Antimicrobial Resistance Surveillance System. Methods Bloodstream S. aureus isolates from six tertiary healthcare institutions in Nigeria collected between 2016 and 2021 were characterized by antimicrobial susceptibility testing and whole-genome sequencing. Bioinformatic analyses were conducted using publicly available pipelines in addition to contextualization with publicly available sequences. Results Of 138 isolates, 85 (61.6%) were methicillin-resistant S. aureus (MRSA). A total of 31 spa types, 14 sequence types (STs), eight clonal complexes (CCs) - CC1, CC5, CC8, CC15, CC30, CC45, CC88, CC121 - and two singletons (ST152 and ST11258) were identified. ST152 (n = 48, 35%) was the predominant lineage, followed by ST772 (n = 21, 15%), ST8 (n = 16, 12%) and ST789 (n = 13, 9%). These lineages were detected across sentinel sites, indicating widespread geographic dissemination. ST772-MRSA isolates possessed the highest number of antimicrobial (AMR) and virulence genes. ST789 was characterized by numerous AMR genes in both MRSA and MSSA backgrounds, whereas ST8 and ST152-MRSA isolates demonstrated abundant virulence genes, with comparatively few AMR genes. ST152, ST772, and ST789 genomes generally clustered together relative to publicly available genomes of the corresponding STs, with lineage-specific subclades differentiated by AMR profiles. Conclusion Predominance of ST152-MRSA, ST772-MRSA, and ST789-MRSA among bloodstream S. aureus isolates in Nigeria is a significant public health concern. Sustained genomic surveillance is critical to inform infection prevention and control in Nigeria.

Research Square
University of Ibadan (NG), University College Hospital, Ibadan (NG), Lagos University Teaching Hospital (NG), Babcock University (NG), Osun State University (NG), University of Oxford (GB), University of Ilorin Teaching Hospital (NG), Nigeria Centre for Disease Control (NG), Obafemi Awolowo University (NG)
Antimicrobial Resistance in Staphylococcus
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