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Whole-Genome Sequencing-Based Resistome Analysis of a Clinical Klebsiella pneumonia | ||
| Archives of Razi Institute | ||
| مقالات آماده انتشار، پذیرفته شده، انتشار آنلاین از تاریخ 23 آبان 1405 اصل مقاله (1.19 M) | ||
| نوع مقاله: Original Articles | ||
| شناسه دیجیتال (DOI): 10.66224/ari.2026.373582.4236 | ||
| نویسندگان | ||
| rohollah kamyabi* 1؛ Saba M Almasi Chegeni2؛ Majid Vahed3؛ MohammadHadi Daneshi4 | ||
| 1Department of Molecular Veterinary Directorate General of Tehran Province | ||
| 2Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iranesh BLVD | ||
| 3Department of Research and Development, Bardia & Artin Gene Company, Room 212, First Floor, Alborz Innovation & Creative Industries Factory, 4th Line, Chalous Beltway, Hessar (Sarjoob), Alborz, Iran | ||
| 4Department of Food Hygiene, Science and Research Branch, Islamic Azad University, Tehran, Iran. | ||
| چکیده | ||
| Introduction:Klebsiella pneumoniae is a major cause of healthcare-associated infections and an important reservoir of antimicrobial resistance (AMR) determinants. Whole-genome sequencing (WGS) enables comprehensive resistome characterization and supports genomic AMR surveillance. This study aimed to characterize the resistome of a clinical K. pneumoniae isolate recovered from a mixed lower respiratory tract specimen using WGS and bioinformatic analysis. Methods: Genomic DNA extracted from the clinical specimen was sequenced on the Illumina NovaSeq 6000 platform. After quality control, high-quality reads were assembled de novo using CLC Genomics Workbench version 20 and mapped against the K. pneumoniae RefSeq genome GCF_000240185.1. Resistome profiling was performed using ShortBRED with the Comprehensive Antibiotic Resistance Database (CARD) to identify and quantify AMR-associated markers. Detected markers were classified according to resistance mechanisms and corresponding antimicrobial classes. Results: In total, 347 AMR markers with a cumulative abundance of 16,124.9 RPKM were identified. The resistome was mainly composed of β-lactamase-associated markers, including blaOXA, blaCTX-M, blaSHV, and blaTEM, together with multidrug efflux-associated markers such as acrA, oqxA, mdfA, and tolC. The polymyxin resistance-associated marker arnT was also detected. β-Lactam antibiotic inactivation and multidrug efflux were the predominant resistance mechanisms. Conclusion: Combining de novo assembly, reference-based mapping, and ShortBRED/CARD resistome profiling enabled comprehensive genomic characterization of AMR-associated markers in K. pneumoniae. The findings highlight the diversity of resistance determinants that may coexist within a clinical isolate and emphasize the value of genomic approaches for AMR assessment. This approach may complement phenotypic testing and contribute to genomic surveillance of clinically relevant antimicrobial resistance. | ||
| کلیدواژه‌ها | ||
| Antimicrobial resistance؛ CARD؛ Klebsiella pneumoniae؛ ShortBRED؛ Whole-genome sequencing | ||
| عنوان مقاله [English] | ||
| بررسی رزیستوم مبتنی بر توالی‌یابی کل ژنوم در یک ایزوله بالینی کلبسیلا پنومونیه | ||
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