Publication: Whole genome sequencing and comparative genomics of extended-spectrum beta-lactamase-producing klebsiella pneumonia
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Date
2022
Authors
Chin, Lim May
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Abstract
Background: Extended-spectrum beta-lactamase Klebsiella pneumoniae (ESBL-KP) has emerged as an important cause of hospital-acquired infections with severe consequences. This study undertook the molecular characterisation of antibiotic resistance (AMR) genes, virulence factors and multilocus sequence type of five clinical isolates of ESBL-KP from Hospital Universiti Sains Malaysia (HUSM) using whole genome sequencing (WGS). Methods: Five pure bacterial isolates obtained from INFORMM BioBank were cultured, and genomic DNA extraction was done. The quantification of extracted DNA was determined on a NanoDrop spectrophotometer with verification by agarose gel electrophoresis. WGS was done using MyGS Microbial Whole genome Nanopore Research-based sequence service. The resulting raw reads were quality-filtered and length-filtered, and de novo assembly was done. Comparative analysis was accomplished using a BLAST-based nucleotide similarity search against references from GenBank. Results: The predominant beta-lactamases were blaCTX-M-15 and blaTEM-1, detected in four local isolates (80%). Other beta-lactamases discovered were blaOXA-1, and blaSHV-187 (40%); blaSHV-2, blaSHV-11, and blaSHV-182 (20%). The blaSHV-2 was discovered in one local isolate and not found in reference isolates. Multiple efflux-pump genes, AcrA, AcrAB, mdtK, TolC, siderophores – entB, iutA, fur, ybtS were detected in all local isolates tested. Four isolates were affiliated with different sequence types, ST29, ST147, ST656, ST3416, and one isolate showed an unknown ST. Conclusion: Our study adds significant DNA sequence data on K. pneumoniae strains of local isolates and has demonstrated the value of WGS in characterising AMR and genomic comparison with other references in GenBank. This helps guide health practitioners’ treatment plans in both critical and non-critical settings within HUSM
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Keywords
Whole genome sequencing , comparative genetics