Frontiers in cellular and infection microbiology · 2026
Distribution of ST116 carbapenem-resistant Citrobacter freundii in public genomes and characterization of a triple-carbapenemase-producing strain.
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Li Wanxiang, Ma Jie, Zhang Cong, Wang Yuhui, Duan Yang
Аннотация
OBJECTIVE: To characterize a carbapenem-resistant Citrobacter freundii (CR-CFR) clinical isolate belonging to the sequence type ST116 and to investigate the public-genome distribution of ST116 among carbapenem-resistant C. freundii.
METHODS: A carbapenem-resistant C. freundii isolate (WF1033) was recovered from a patient with a urinary tract infection. Antimicrobial susceptibility testing, whole-genome sequencing, and detailed plasmid structural analyses were performed. To contextualize this isolate, a large-scale genomic analysis of publicly available CR-CFR genomes was conducted, including multilocus sequence typing (MLST), minimum spanning tree analysis, global distribution mapping, and phylogenetic reconstruction of sequence type ST116.
RESULTS: WF1033 exhibited an extensively drug-resistant phenotype and harbored three carbapenemase genes, bla KPC-2, bla IMP-8, and bla NDM-1. Genomic analysis revealed that WF1033 belongs to ST116 and carries four plasmids. Notably, bla KPC-2 and bla IMP-8 were co-located on a novel hybrid IncFIB/IncFII plasmid (pWF1033-KPC-IMP), formed through the integration of distinct mobile genetic elements, whereas bla NDM-1 was carried on a typical IncX3 plasmid. Analysis of 2,436 CR-CFR genomes identified 171 sequence types, with ST22 being the most prevalent globally. However, ST116 showed marked regional enrichment in China, accounting for 56.97% of all ST116 isolates. ST116 also displayed a higher proportion of strains carrying multiple carbapenem resistance genes (CRGs) compared with other major sequence types. Phylogenetic analysis of 165 ST116 isolates revealed multiple clades, suggesting possible lineage expansion and geographic persistence within this sequence type, with WF1033 representing the only ST116 strain identified to date carrying three CRGs simultaneously.
CONCLUSIONS: Our findings suggest that ST116 represents a lineage associated with increased carriage of multiple carbapenem resistance genes in CR-CFR. Continuous genomic surveillance is warranted to monitor the dissemination of multidrug-resistant C. freundii, particularly among ST116-associated lineages.
METHODS: A carbapenem-resistant C. freundii isolate (WF1033) was recovered from a patient with a urinary tract infection. Antimicrobial susceptibility testing, whole-genome sequencing, and detailed plasmid structural analyses were performed. To contextualize this isolate, a large-scale genomic analysis of publicly available CR-CFR genomes was conducted, including multilocus sequence typing (MLST), minimum spanning tree analysis, global distribution mapping, and phylogenetic reconstruction of sequence type ST116.
RESULTS: WF1033 exhibited an extensively drug-resistant phenotype and harbored three carbapenemase genes, bla KPC-2, bla IMP-8, and bla NDM-1. Genomic analysis revealed that WF1033 belongs to ST116 and carries four plasmids. Notably, bla KPC-2 and bla IMP-8 were co-located on a novel hybrid IncFIB/IncFII plasmid (pWF1033-KPC-IMP), formed through the integration of distinct mobile genetic elements, whereas bla NDM-1 was carried on a typical IncX3 plasmid. Analysis of 2,436 CR-CFR genomes identified 171 sequence types, with ST22 being the most prevalent globally. However, ST116 showed marked regional enrichment in China, accounting for 56.97% of all ST116 isolates. ST116 also displayed a higher proportion of strains carrying multiple carbapenem resistance genes (CRGs) compared with other major sequence types. Phylogenetic analysis of 165 ST116 isolates revealed multiple clades, suggesting possible lineage expansion and geographic persistence within this sequence type, with WF1033 representing the only ST116 strain identified to date carrying three CRGs simultaneously.
CONCLUSIONS: Our findings suggest that ST116 represents a lineage associated with increased carriage of multiple carbapenem resistance genes in CR-CFR. Continuous genomic surveillance is warranted to monitor the dissemination of multidrug-resistant C. freundii, particularly among ST116-associated lineages.
Предметные рубрики MeSH
Citrobacter freundiibeta-LactamasesPlasmidsPhylogenyBacterial ProteinsMicrobial Sensitivity TestsGenome, BacterialHumansMultilocus Sequence TypingWhole Genome SequencingCarbapenemsAnti-Bacterial AgentsCarbapenem-Resistant EnterobacteriaceaeEnterobacteriaceae InfectionsUrinary Tract InfectionsDrug Resistance, Multiple, Bacterial