Deciphering the genomic character of the multidrug-resistant <i>Staphylococcus aureus</i> from Dhaka, Bangladesh

Afia Anjum; Jarin Tabassum; Sohidul Islam; A. K. M. Imrul Hassan; Ishrat Jabeen; Sabbir R. Shuvo; Afia Anjum; Jarin Tabassum; Sohidul Islam; A. K. M. Imrul Hassan; Ishrat Jabeen; Sabbir R. Shuvo

doi:10.3934/microbiol.2024036

AIMS Microbiology

2024, Volume 10, Issue 4: 833-858. doi: 10.3934/microbiol.2024036

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Research article

Deciphering the genomic character of the multidrug-resistant Staphylococcus aureus from Dhaka, Bangladesh

Department of Biochemistry & Microbiology, North South University, Dhaka, Bangladesh
These two authors contributed equally.

Received: 05 April 2024 Revised: 02 September 2024 Accepted: 20 September 2024 Published: 29 September 2024

Staphylococcus aureus is one of the leading agents of nosocomial and community-acquired infections. In this study, we explored the genomic characterization of eight methicillin-resistant clinical isolates of S. aureus from Dhaka, Bangladesh. Notably, all strains were resistant to penicillin, cephalosporins, and monobactams, with partial susceptibility to meropenem and complete susceptibility to amikacin, vancomycin, and tigecycline antibiotics. The strains were found to have an average genome size of 2.73 Mbp and an average of 32.64% GC content. Multi-locus sequence typing analysis characterized the most predominant sequence type as ST361, which belongs to the clonal complex CC361. All isolates harbored the mecA gene, often linked to SCCmec_type IV variants. Multidrug resistance was attributed to efflux pumps NorA, NorC, SdrM, and LmrS alongside genes encoding beta-lactamase BlaZ and factors like ErmC and MepA. Additionally, virulence factors including adsA, sdrC, cap8D, harA, esaA, essC, isdB, geh, and lip were commonly identified. Furthermore, genes associated with heme uptake and clumping were present, highlighting their roles in S. aureus colonization and pathogenesis. Nine secondary metabolite biosynthetic gene clusters were found, of which six were common in all the strains. Numerous toxin-antitoxin systems were predicted, with ParE and ParB-like nuclease domains found to be the most prevalent toxin and antitoxin, respectively. Pan-genome analysis revealed 2007 core genes and 229 unique genes in the studied strains. Finally, the phylogenomic analysis showed that most Bangladeshi strains were grouped into two unique clades. This study provides a genomic and comparative insight into the multidrug resistance and pathogenicity of S. aureus strains, which will play a crucial role in the future antibiotic stewardship of Bangladesh.
- S. aureus,
- Bangladesh,
- MRSA,
- phylogenomic,
- resistance mechanisms
Citation: Afia Anjum, Jarin Tabassum, Sohidul Islam, A. K. M. Imrul Hassan, Ishrat Jabeen, Sabbir R. Shuvo. Deciphering the genomic character of the multidrug-resistant Staphylococcus aureus from Dhaka, Bangladesh[J]. AIMS Microbiology, 2024, 10(4): 833-858. doi: 10.3934/microbiol.2024036

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Abstract

Staphylococcus aureus is one of the leading agents of nosocomial and community-acquired infections. In this study, we explored the genomic characterization of eight methicillin-resistant clinical isolates of S. aureus from Dhaka, Bangladesh. Notably, all strains were resistant to penicillin, cephalosporins, and monobactams, with partial susceptibility to meropenem and complete susceptibility to amikacin, vancomycin, and tigecycline antibiotics. The strains were found to have an average genome size of 2.73 Mbp and an average of 32.64% GC content. Multi-locus sequence typing analysis characterized the most predominant sequence type as ST361, which belongs to the clonal complex CC361. All isolates harbored the mecA gene, often linked to SCCmec_type IV variants. Multidrug resistance was attributed to efflux pumps NorA, NorC, SdrM, and LmrS alongside genes encoding beta-lactamase BlaZ and factors like ErmC and MepA. Additionally, virulence factors including adsA, sdrC, cap8D, harA, esaA, essC, isdB, geh, and lip were commonly identified. Furthermore, genes associated with heme uptake and clumping were present, highlighting their roles in S. aureus colonization and pathogenesis. Nine secondary metabolite biosynthetic gene clusters were found, of which six were common in all the strains. Numerous toxin-antitoxin systems were predicted, with ParE and ParB-like nuclease domains found to be the most prevalent toxin and antitoxin, respectively. Pan-genome analysis revealed 2007 core genes and 229 unique genes in the studied strains. Finally, the phylogenomic analysis showed that most Bangladeshi strains were grouped into two unique clades. This study provides a genomic and comparative insight into the multidrug resistance and pathogenicity of S. aureus strains, which will play a crucial role in the future antibiotic stewardship of Bangladesh.

Acknowledgments

We would like to thank North South University (grant number NSU: CTGRC-21-SHLS-05 to SRS) for the financial support of this work. Also, we thank Ms. Munmun Faria Iqbal and Ms. Sadia Ferdous from the Department of Biochemistry & Microbiology, North South University, for assistance with the isolation of the strains and broth microdilution techniques for MIC determination, respectively.

Conflict of interest

All authors declare no conflicts of interest in this paper.

Author contributions

This research was conceptualized by SRS. Formal analysis, comparative genome analysis, and data visualization were conducted by AA, JT, and AKH. Methodology and supervision were performed by SRS, SI. The manuscript was written by AA, JT, SI, SRS, and IJ. All authors read and approved of the final manuscript.

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