Adaptive colistin resistance dynamics in mcr-9-positive and -negative Enterobacterales following low-level colistin...

The mcr-9 gene has been reported across different sources and was recognized as a potential contributor to increased minimum inhibitory concentrations after colistin exposure. This study aimed to determine the prevalence of intestinal carriage of the mcr-9 gene in hospitalized patients and characterize the genomic features of mcr-9-carrying Enterobacterales. From December 2019 to November 2020, rectal swabs were enriched and screened for the mcr-9 gene using qPCR. PCR-positive broths were cultured on chromogenic agar, and mcr-9-positive isolates underwent whole-genome sequencing and antimicrobial susceptibility testing. Colistin susceptibility was reassessed after exposure to subinhibitory concentrations of colistin, including mcr-9-negative control isolates. Of 624 rectal swabs, 22 (3.5%) were mcr-9-positive, and 9 colistin-susceptible Enterobacterales were cultured. Following colistin exposure, resistance developed in 6/9 mcr-9-positive isolates and remained stable in 5/6 after 10 days of subcultivation on media without colistin; mutations in genes related to colistin resistance were identified. Colistin resistance also emerged in 4/7 mcr-9-negative isolates, with stable resistance observed in two. Exposure to low colistin concentrations can select for transient or stable resistance in Enterobacterales through diverse adaptive mechanisms. This phenomenon occurred in both mcr-9-positive and mcr-9-negative isolates and varied across strains, indicating that mcr-9 presence alone does not predict adaptive outcomes. The heterogeneity in stability and reversibility of resistance suggests strain-specific genetic backgrounds and evolutionary fitness-related processes that warrant further investigation.IMPORTANCEThis study investigates the prevalence and genomic characteristics of mcr-9-carrying Enterobacterales in hospitalized patients, marking the first such screening in this population. Although the mcr-9 gene is often associated with colistin-susceptible isolates, previous studies have suggested that exposure to colistin may be associated with increased minimum inhibitory concentrations in mcr-9-positive isolates. Our findings demonstrate that exposure to low colistin concentrations can select for colistin resistance in both mcr-9-positive and mcr-9-negative Enterobacterales, highlighting a heterogeneous and strain-dependent adaptive response. These resistance dynamics were primarily associated with mutations in regulatory systems such as PmrAB and PhoPQ and were not uniformly stable, with some isolates reverting to colistin susceptibility following growth in colistin-free media. This observation is clinically relevant, as subinhibitory colistin concentrations, commonly encountered due to unfavorable pharmacokinetics and dose-limiting nephrotoxicity, may inadvertently promote the emergence of adaptive resistance during treatment.