Nanopore sequencing of antibiotic-resistant Klebsiella pneumoniae JRCGR1 isolate from Pakistan and country scale pan-genomics

Klebsiella pneumoniae is a gram-negative, encapsulated, non-motile bacterium that can cause damage to human lungs. Antibiotic resistance of this strain requires constant monitoring and for this purpose, Oxford nanopore mediated whole genome sequencing was done for a strain acquired from the pleural fluid of a diabetic patient suffering from chronic kidney disease. A genome of 5.98 MB was obtained, with 8,869 CDSs and 110 RNAs. Around 96 proteins were seen as involved in virulence, disease or defense, while 25 antibiotic resistance genes were identified. Pan-genome was inferred as open, with 12,857 and 1,303 CDSs forming respective accessory and core genome of antibiotic resistant Pakistani strains (n=168) of this species. Apart from notable antimicrobial resistance genes like beta-lactamases, a gene conferring resistance to colistin was also mined. To the best of our knowledge, this is first report of nanopore mediated long read sequencing of a hypermucoviscous virulent K. pneumoniae from Pakistan.