Genomic characterization of colistin heteroresistance in Klebsiella pneumoniae during a nosocomial outbreak

Klebsiella pneumoniae is emerging as an important nosocomial pathogen due to its rapidly increasing resistance to nearly all currently available antibiotics. This resistance highlights the therapeutic role of last-resort polymyxin-antibiotics such as colistin. However, heteroresistance, defined as a mixture of susceptible and resistant populations, may hamper the effectiveness of treatment in patients with multidrug-resistant organism infections. In a previous study, we have shown that colistin resistance among extended-spectrum beta-lactamase -producing K. pneumoniae (ESBL-Kp) isolates emerged after the introduction of Selective Digestive Tract Decontamination (SDD) in an Intensive Care Unit (ICU). In this study, we further investigated through population analysis profiles (PAP) the possible role of heteroresistance among these isolates in the emergence of colistin resistance, and we used whole genome sequencing (WGS) to identify the mechanisms by which colistin resistance in K. pneumoniae can emerge de novo. PAPs were conducted for five colistin-susceptible isolates from different patients, one was obtained before the introduction of SDD and four thereafter. In all five isolates, heteroresistant subpopulations grew in the presence of colistin. WGS revealed the presence of mutations in lpxM, mgrB, phoQ, and yciM genes. In conclusion, the present study shows that heteroresistance is the underlying mechanism for the emergence of colistin resistance among ESBL-producing K. pneumoniae obtained from ICU patients who had been exposed to colistin.