Colistin Heteroresistance Is Largely Undetected among Carbapenem-Resistant Enterobacterales in the United States

Abstract

Heteroresistance is a form of antibiotic resistance where a bacterial strain is comprised of a minor resistant subpopulation and a majority susceptible subpopulation. We showed previously that colistin heteroresistance can mediate the failure of colistin therapy in an in vivo infection model, even for isolates designated susceptible by clinical diagnostics. We sought to characterize the extent of colistin heteroresistance among the highly drug-resistant carbapenem-resistant Enterobacterales (CRE). We screened 408 isolates for colistin heteroresistance. These isolates were collected between 2012 and 2015 in eight U.S. states as part of active surveillance for CRE. Colistin heteroresistance was detected in 10.1% (41/408) of isolates, and it was more common than conventional homogenous resistance (7.1%, 29/408). Most (93.2%, 38/41) of these heteroresistant isolates were classified as colistin susceptible by standard clinical diagnostic testing. The frequency of colistin heteroresistance was greatest in 2015, the last year of the study. This was especially true among Enterobacter isolates, of which specific species had the highest rates of heteroresistance. Among Klebsiella pneumoniae isolates, which were the majority of isolates tested, there was a closely related cluster of colistin-heteroresistant ST-258 isolates found mostly in Georgia. However, cladistic analysis revealed that, overall, there was significant diversity in the genetic backgrounds of heteroresistant K. pneumoniae isolates. These findings suggest that due to being largely undetected in the clinic, colistin heteroresistance among CRE is underappreciated in the United States.IMPORTANCE Heteroresistance is an underappreciated phenomenon that may be the cause of some unexplained antibiotic treatment failures. Misclassification of heteroresistant isolates as susceptible may lead to inappropriate therapy. Heteroresistance to colistin was more common than conventional resistance and was overwhelmingly misclassified as susceptibility by clinical diagnostic testing. Higher proportions of colistin heteroresistance observed in certain Enterobacter species and clustering among heteroresistant Klebsiella pneumoniae strains may inform colistin treatment recommendations. Overall, the rate of colistin nonsusceptibility was more than double the level detected by clinical diagnostics, suggesting that the prevalence of colistin nonsusceptibility among CRE may be higher than currently appreciated in the United States.

Keywords: CRE; Enterobacterales; Enterobacteriaceae; antibiotic resistance; colistin; heteroresistance; polymyxins.

FIG 1

Rate of colistin heteroresistance by genus, year, and clinical detection. (A) Table of colistin heteroresistance incidence by the indicated genus, species, and P value for the odds ratio in each category. (B) Incidence of total colistin-heteroresistant isolates as a percentage in each year from 2012 to 2015. *, P < 0.05 for the positive linear trend from 2012 to 2015 (Cochran-Armitage trend test). (C) Proportion of isolates designated colistin susceptible (green) or colistin resistant (red) by standard clinical susceptibility testing. The portion with hatched lines indicates isolates that were heteroresistant by population analysis profile. The right margin represents the clinical designations of all colistin-heteroresistant isolates.

FIG 2

Colistin heteroresistance in K. pneumoniae occurs in genetically diverse isolates and forms a cluster of related isolates in Georgia. (A) Cladistic analysis of colistin-heteroresistant K. pneumoniae isolates by whole-genome sequence, with the corresponding sequence type and capsule type for each isolate. A closely related cluster of ST-258 isolates is highlighted in blue. (B) Cladistic analysis of all K. pneumoniae isolates in the study.