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

Two bacterial strains were recovered from the same catheter specimen of urine sample. TheEscherichia coli strain encoded 11 resistance genes on a plasmid, including the ESBL gene,blaCTX-M-15. TheKlebsiella pneumoniae strain encoded an additional 5 resistance genes on a plasmid, including 2 copies ofblaCTX-M-15. Resistance genes were flanked between IS26 in a multimeric array. Both plasmids were similar, suggesting horizontal transfer occurred during the course of infection. AbstractEscherichia coli andKlebsiella 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 theK. pneumoniae strain, additionally encoded the five  AMR genes:sul2, strA, strB, blaTEM-1B, andblaCTX-M-15. A multimeric array of AMR genes and IS26 insertion sequences were found in the plasmids from both isolat...
Source: MicrobiologyOpen - Category: Microbiology Authors: Tags: COMMENTARY Source Type: research