Genomic analyses of an Escherichia coli and Klebsiella pneumoniae urinary tract co-infection using long-read nanopore sequencing

Abstract

Escherichia coli and Klebsiella pneumoniae isolates presenting with the same antimicrobial susceptibility profile were recovered from the same catheter sample of urine (CSU). Both strains were recovered from a patient with a long-standing indwelling urinary catheter. Each isolate had its DNA extracted following culture. Nanopore long-read sequencing was used to build the plasmids and chromosomes from each strain to closure to discern the potential horizontal propagation of resistance-encoding plasmids and the relationship between resistance genes and insertion sequences. Plasmids derived from resistance strains in the urinary microbiota remain poorly characterized. The same 11 antimicrobial resistance (AMR) genes were found in plasmids from each strain. The 185,239-bp FIB(K) pKBM1, from the K. pneumoniae strain, additionally encoded the five AMR genes: sul2, strA, strB, bla_TEM-1B, and bla_CTX-M-15. A multimeric array of AMR genes and IS26 insertion sequences were found in the plasmids from both isolates. Both plasmids from each isolate were similar. Horizontal transfer of plasmids, followed by subsequent plasmid rearrangement, is likely to have occurred during infection. Furthermore, the resistance region in the plasmids shared similarity against the internationally prevalent plasmid, pKPN3-307_typeA, commonly identified in K. pneumoniae ST307. Biofilm formation in catheterized patients may allow close cell contact between strains. Horizontal propagation of resistance genes may occur, leading to polymicrobial infections.