Draft genome sequence of an extensively drug-resistant neonatal Klebsiella pneumoniae isolate harbouring multiple plasmids contributing to antibiotic resistance

• Main Authors: Sidra Rahmat Ullah, Mahnoor Majid, Saadia Andleeb
• Format: Article
• Language: English
• Published: Elsevier 2020-12-01
• Series: Journal of Global Antimicrobial Resistance
• Subjects: Antibiotic resistance; Neonatal Klebsiella pneumoniae; Nosocomial infection; Whole-genome sequencing; XDR; Plasmid
• Online Access: http://www.sciencedirect.com/science/article/pii/S2213716520302137

Objectives: Klebsiella pneumoniae is a notorious nosocomial pathogen that has become a significant cause of neonatal infections causing morbidity and mortality. A multidrug-resistant K. pneumoniae isolate (K184) was isolated from a 5-day-old infant admitted to the neonatal intensive care unit of a local hospital in Rawalpindi, Pakistan. Whole-genome analysis of the isolated strain was performed to gain a better understanding of the genetic basis of antimicrobial resistance and virulence determinants. Methods: K. pneumoniae isolate K184 was sequenced on an Illumina HiSeq 2500 platform. The genome was assembled using SPAdes with 30× coverage and was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.4.3. Characterisation of the strain was performed using MLST 2.0 server. Plasmids, antimicrobial resistance determinants and virulence factors were identified using PlasmidFinder v.2.0, the Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factors Database (VFDB), respectively. Results: Neonatal K. pneumoniae isolate K184 has a considerably large genome with a size of 6,686,067 bp and a GC content of 55.6%. The isolate possesses three plasmids actively contributing to antimicrobial resistance, which classifies it as heavily loaded genome, along with three prophage regions. With 15 antimicrobial resistance determinants and various virulence factors, the neonatal isolate belongs to ST2096. Conclusion: The genome of neonatal isolate K184 studied here provides an insight into antibiotic resistance and virulence determinants. This draft genome can be used to compare antimicrobial-resistant K. pneumoniae strains isolated from the neonatal population.