Emergence of transmissible mcr-9.1 plasmids in clinical Cronobacter sakazakii : CRISPR typing unravels phage-driven evolution and high-risk lineage

Cronobacter spp. is an important foodborne pathogen that causes serious neonatal infections. The prevalence of the colistin resistance gene mcr-9 in Cronobacter spp. strains isolated from foods has been reported; however, there are no reports for isolates from clinical infections. Surveillance of Cronobacter infection was conducted at a prominent children’s hospital in China during 2015–2023 and also in a tertiary hospital in 2023. There were a total of seven Cronobacter sakazakii infection cases, and mcr-9.1 was detected in one ST13 and two ST256 strains. After adding the publicly available sequence data, the backbones of IS 1R-mcr-9.1-wbuc-qsec in C. sakazakii ST13 and IS 903B-mcr-9.1-wbuc -IS 26 in ST256 strains are proposed to be associated with IncFIB and IncHI2 plasmids, respectively. More importantly, the mcr-9.1 -positive IncHI2 plasmid in C. sakazakii ST256 clinical strain can be transferred to Escherichia coli J53, conferring multiple drug resistance. These ST13 and ST256 strains were assigned to 19 CRISPR types (CTs), and mcr-9.1 -positive strains belonged to specific CTs in China. While ST256 has not been detected in contaminated food, its presence in insect and environmental samples suggests a potential transmission route requiring further investigation. Combined phylodynamic and CRISPR spacer analyses suggested phage interactions shaped C. sakazakii ST13 evolution. The relatively high-risk lineage bridging clinical ( mcr-9.1 -positive CT212) and food chain (CT208) reservoirs displayed CRISPR adaptation signatures: selective type 1 ancestral spacer loss coupled with type 2 ancestral preservation. Plasmid-mediated mcr-9.1 gene transfer in C. sakazakii poses a potential threat to public health, thereby necessitating vigilant clinical monitoring. IMPORTANCE Cronobacter spp. is ubiquitous in food and the environment, although the infection incidence of this pathogen is low, the case-fatality rate is high in premature and immunocompromised infants. In this study, we first report that the silent dissemination of mcr-9.1 in Cronobacter sakazakii ST13 and ST256 strains was associated with IncFIB and IncHI2 plasmids, respectively. The mcr-9.1 -encoding IncHI2 plasmid was transferable from the ST256 strain, suggesting significant dissemination potential among clinically relevant bacteria. Taking into account the temporal organization of spacers, we first used CRISPR diversity to trace the origins of mcr-9.1 -positive C. sakazakii strains and deduce their divergent evolution through the preserved spacer information targeting specific phages. Our CRISPR-enhanced molecular epidemiology approach enables robust phylogenetic inferences despite limited clinical isolates, demonstrating a transferable framework applicable to other emerging pathogens with surveillance data.