Epidemiology, phylogeny and genetic characterization of carbapenem-resistant Citrobacter spp. from 5 hospitals in China

Abstract

Objectives

Carbapenem-resistant Citrobacter spp. (CRC) are increasingly recognized as healthcare-associated pathogens, while systematic studies on clinical epidemiology, genetic diversity, and resistant mechanisms of CRC are relatively scarce. The present study provides comprehensive and systematic research on CRC.

Methods

Clinical isolates of Citrobacter spp. resistant to carbapenems were collected from 5 hospitals across China between October 2014 and December 2017. All the isolates were identified by MALDI-TOF MS and FastANI. Whole-genome sequencing and phylogenetic analyses were performed. Sequencing data were analyzed using MLST, PlasmidFinder, ResFinder, and ISFinder tools.

Results

Thirty-one CRC isolates were isolated from 5 hospitals in different provinces. These strains exhibited significant phylogenetic divergence. ST85 (12.90%) and ST116 (12.90%) were the predominant STs. NDM (41.94%), KPC-2 (25.81%), and IMP (19.35%) were the most frequent carbapenemases of CRC. Interestingly, KPC is frequently associated with C. freundii, while NDM is predominantly observed in C. portucalensis. All the IncX3 and IncN-type plasmids carrying bla_NDM and most non-typeplasmids carrying bla_KPC were transferrable by conjugation. The genes bla_NDM and bla_KPC were primarily located within relatively conserved genomic environments, including “ISAba125-bla_NDM-ble_MBL-trpF-dsbD-cutA1-groES-groEL-ISCR27” and “Tn3 transposase-ISKpn27-bla_KPC-2-△ISKpn6-korC-kclA-hp-hp-△repB-TnAS1”.

Conclusions

The clonal transmission of CRC and the conjugative antibiotic resistance plasmids were the key mechanisms driving the spread of multidrug resistance. It highlights the need to strengthen molecular surveillance, with a focus on high-prevalence clones such as ST85 and ST116 carrying mobile resistance elements.