ABSTRACT
We report the draft genome sequence of the methicillin-resistant Staphylococcus aureus (MRSA) strain MRSA_GSTU_PS9_BD, isolated from a patient’s wound infection in Bangladesh. The genome harbors 123 and 22 predicted virulence factors and antimicrobial resistance genes, respectively, with a 91.86% probability of being a human pathogen.
KEYWORDS: antibiotic resistance, mecA, Staphylococcus aureus, methicillin resistance, genomes
ANNOUNCEMENT
Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium that poses a serious threat in healthcare facilities and community settings due to its resistance to multiple antibiotics. It is a global concern that requires careful consideration and effective therapeutic approaches (1, 2). MRSA strains are currently causing a significant 25%–50% of clinical S. aureus infections in different countries (3). Annually, there are over 80,000 new cases of MRSA acquired in hospitals, along with more than 11,000 deaths related to hospital-associated MRSA (4).
Staphylococcus aureus MRSA_GSTU_PS9_BD was isolated from wound infections in Gopalganj Sadar Hospital, Bangladesh in 2024. Wound swabs were collected aseptically in Falcon tubes containing phosphate-buffered saline and transferred to the Microbiology Laboratory at the Department of Biotechnology and Genetic Engineering, Gopalganj Science and Technology University, Gopalganj-8105, Bangladesh, where presumptive identification of S. aureus was first performed by standard cultural, morphological, biochemical, and molecular assays. Antimicrobial susceptibility testing was performed via the Kirby-Bauer disk diffusion technique. Methicillin resistance was confirmed by PCR targeting the mecA gene. Among the identified isolates, Staphylococcus aureus MRSA_GSTU_PS9_BD exhibited extensive multidrug resistance and was therefore selected for whole-genome sequencing (WGS) to evaluate its antimicrobial resistance patterns, virulence profiles, and genomic characteristics essential to public health surveillance. S. aureus strain MRSA_GSTU_PS9_BD was cultured overnight on nutrient agar at 37°C. The isolate was submitted for WGS to the Genome Center of the International Center for Diarrhoeal Disease Research, Bangladesh. Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (cat. A1620; Promega, Madison, WI, USA), and the DNA library was prepared using Illumina DNA Prep (Illumina, San Diego, CA, USA). Sequencing was carried out on the Illumina NextSeq 2000 platform, generating Illumina paired-end raw 2 × 150 bp reads. The raw reads were quality controlled using FastQC v0.12.1 (5) and trimmed using fastp v0.23.4 (6). De novo assembly was performed using SPAdes v3.15.5 (7, 8) and classified using Kraken2 v2.1.3 (9).
The detailed genomic characteristics of the isolated S. aureus strain MRSA_GSTU_PS9_BD are summarized in Table 1. The BV-BRC (10) and the NCBI Prokaryotic Genome Annotation Pipeline v6.10 (11) were used to resolve a final genome of 34 contigs with a total length of 2,846,816 bp and a GC content of 32.68%. Analysis of the assembled contig with PathogenFinder v2.0 (12) showed the isolate had a 91.86% probability of being a human pathogen. Analysis with RGI main from CARD v4.0.2 (13) identified 22 AMR genes, including blaZ, mecA, erm(C), tet(K), and dfrG. Virulence Factors Database (14) predicted 123 VFs genes, including coa, hlgA-C, lukF-PV, lukS-PV, and sep. The MLSTFinder v1.0.1 (15) from the CGE web server revealed that our sequence type is ST2884, which was the most prevalent lineage of S. aureus in this region. Default parameters were applied for all software unless otherwise specified.
TABLE 1.
Genomic characteristics of S. aureus strain MRSA_GSTU_PS9_BD isolated from wound infections
| Attributes | Values |
|---|---|
| BioProject accession no. | PRJNA1445818 |
| BioSample accession no. | SAMN56799133 |
| GeneBank accession no. | JBWQPW000000000 |
| SRA accession no. | SRR37920994 |
| Contigs | 34 |
| Genome size (bp) | 2,846,816 |
| GC content (%) | 32.68 |
| Contig L50 | 3 |
| Contig N50 | 284,088 |
| Coverage (×) | 125.6 |
| Sequence completeness (%) | 99.51 |
| Genes (total) | 2,895 |
| CDS (total) | 2,832 |
| Genes (coding) | 2,750 |
| Total RNAs | 63 |
| No. of tRNAs | 56 |
| No. of rRNAs | 3 |
| No. of ncRNAs | 4 |
| No. of pseudogenes (total) | 82 |
| Pseudogenes (ambiguous residues) | 0 |
| Pseudogenes (frameshifted) | 35 |
| Pseudogenes (incomplete) | 43 |
| Pseudogenes (internal stop) | 19 |
| No.of hypothetical proteins | 561 |
| No. of AMR genes | 22 |
| No. of VFs genes | 123 |
| No. of intact prophage regions | 3 |
ACKNOWLEDGMENTS
The authors would like to express their gratitude to the Department of Biotechnology and Genetic Engineering, Gopalganj Science and Technology University, Gopalganj-8105, Bangladesh, and Biomedical and Toxicological Research Institute, Bangladesh Council of Scientific and Industrial Research, Dhaka-1205, Bangladesh, for providing the facilities.
This study was partially supported by funding from Research Center, Gopalganj Science and Technology University (grant no. BSMRSTU-RC-24-039) provided by University Grants Commission of Bangladesh .
Contributor Information
Md. Abdurrahim, Email: rahim.phr@gmail.com.
Md. Sahabuddin, Email: sahabuddin@gstu.edu.bd.
André O. Hudson, Rochester Institute of Technology, Rochester, New York, USA
DATA AVAILABILITY
The Whole-Genome Shotgun Sequencing Project for the Staphylococcus aureus strain MRSA_GSTU_PS9_BD has been deposited in DDBJ/ENA/GenBank under accession number JBWQPW000000000 and in the Sequence Read Archive under BioProject accession number PRJNA1445818.
ETHICS APPROVAL
The ethics clearance committee of Gopalganj Science and Technology University, Gopalganj-8105, Bangladesh, approved the study (registration no. BSMRSTU-RC/ECC/24/039).
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Associated Data
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Data Availability Statement
The Whole-Genome Shotgun Sequencing Project for the Staphylococcus aureus strain MRSA_GSTU_PS9_BD has been deposited in DDBJ/ENA/GenBank under accession number JBWQPW000000000 and in the Sequence Read Archive under BioProject accession number PRJNA1445818.