Identification of OqxB Efflux Pump and Tigecycline Resistance Gene Cluster in Multidrug-Resistant Isolate G3.

PURPOSE

To identify antibiotic resistance genes (ARGs) and understand the molecular basis of multidrug resistance in isolate G3.

METHODS

Whole-genome sequencing of isolate G3 was conducted at 30X coverage using Illumina NovaSeq 6000. Reads were trimmed using Trimmomatic and assessed using a combination of scripts that incorporated Samtools, BedTools, and bwa-mem. assembly was performed using SPAdes, and assembly metrics were evaluated using QUAST. The assembled genome was uploaded to a Type Strain Genome Server (TYGS) for taxonomic identification. Genome annotation was performed using the KBase and Proksee software using PROKKA. ARGs were identified using the Comprehensive Antibiotic Resistance Database (CARD).

RESULTS

isolate G3 demonstrated resistance to most antibiotics tested, including meropenem (10 µg), ciprofloxacin (5 µg), gentamicin (10 µg), and tetracycline (30 µg). The ARGs identified were , and . A tigecycline-resistant gene cluster, , was found in NODE_84, while the gene, encoding a resistance-nodulation-division (RND) efflux pump, was in NODE_309. Phylogenetic analysis showed clustered with species, distinct from and . Comparative analysis of revealed isolate G3 shared 78-100% identity with strain 1334/14 in key components of the multidrug efflux system, including the transcriptional regulator , periplasmic adaptor subunit , and permease subunit .

CONCLUSION

Our findings offer new insights into the reservoir of ARGs in the draft genome of isolate G3, including the and genes, highlighting its genomic plasticity and public health significance. This adaptability enables to thrive in clinical environments, despite its natural habitat association. This study advances our understanding of the molecular mechanisms driving resistance in and offers valuable insights to inform strategies for combating the spread of antimicrobial resistance in clinical and environmental settings.