Whole-genome sequencing and genomic characterization of a novel multi-drug resistant esxA-positive Staphylococcus haemolyticus DUEML1 (ST-184) isolated from a respiratory infection case: insights from panresistome analysis

Staphylococcus haemolyticus is a coagulase-negative staphylococcal species and an opportunistic pathogen associated with hospital-acquired infections. The aim of this study was to use whole-genome sequencing (WGS) to characterize a novel multidrug-resistant (MDR) S. haemolyticus strain, DUEML1 (ST-184), isolated from a respiratory infection case in Bangladesh, and to place its resistome and virulence features in the context of global S. haemolyticus isolates. The isolate was obtained in pure culture from the tracheal aspirate of a 51-year-old male patient with respiratory infection, suggesting it was the primary causative agent. WGS was the primary method to analyze the genome of the isolated strain and subsequent in-silico analyses were performed to identify antimicrobial resistance genes, virulence factors, plasmid-associated genes, mobile genetic elements (MGEs), and prophages. Comparative pan-resistome analysis was conducted using 694 publicly available S. haemolyticus genomes retrieved from NCBI. The isolate exhibited in vitro resistance to levofloxacin, ciprofloxacin, tetracycline, doxycycline, gentamicin, and trimethoprim-sulfamethoxazole, as determined by the disc diffusion test, and demonstrated the capacity for biofilm formation. Several antimicrobial resistance genes (ARGs) such as fosBx1, mgrA, norC, sdrM, sepA and two virulence genes, including esxA and cap8G were detected. To our knowledge, this is the first report of an esxA-positive S. haemolyticus isolate, recovered from a respiratory infection case in Dhaka, Bangladesh. Two plasmid-associated genes repUS23 and repUS46 were detected. Further analyses predicted 63 horizontal gene transfer (HGT) events and identified 147 MGEs, including integration/excision elements, recombination and repair-associated genes, and prophage-associated regions. With a new variant of arcC allele (arcC-38), the isolate was assigned to a novel ST-184. The PathogenFinder predicted a 93% probability that ST-184 is a human pathogen. A comparative analysis of 694 genome sequences identified a wide variety of ARGs, virulence factors, and plasmids in S. haemolyticus isolates from 35 different countries. This study provides the first genomic characterization of a novel S. haemolyticus ST-184 isolate from Bangladesh, highlighting its multidrug-resistant nature and virulence potential. A limitation of this work is the lack of clinical treatment outcome data. Future research should include large-scale genomic surveillance to strengthen our understanding of the genomic architecture of S. haemolyticus.