Genomic epidemiology of Carbapenem-Resistant Enterobacterales in southern Vietnam: dominance of Klebsiella pneumoniae ST16 and horizontal gene transfer

Background: Carbapenem-resistant Enterobacterales (CRE) pose a critical global threat.However, the genomic epidemiology, transmission dynamics (clonal vs. horizontal gene transfer), and mechanisms driving co-resistance in Southern Vietnam remain poorly understood.This study aimed to use Whole-Genome Sequencing (WGS) to characterize the molecular epidemiology, transmission mechanisms, and co-resistance patterns of CRE from a major referral center in Southern Vietnam Methodology: We performed a cross-sectional study using whole-genome sequencing on 189 CRE isolates (K.pneumoniae, E. coli, E. cloacae) from a major referral hospital in Southern Vietnam.We analyzed Carbapenemase-Producing Genes (CPGs), MLST, colistin resistance mutations, plasmid clusters, and co-carried AMR genes.Results: K. pneumoniae ST16 (n=67, 35.4%) was the most frequently identified clone, detected in 10/12 ward strata.We identified two distinct colistin resistance pathways linked to CPG lineage: bla KPC /bla OXA-48 fam-ily clones (ST147, ST5815, ST11) showed a universal prevalence of chromosomal pmrB mutations (n=55/55, 100%), whereas the bla NDM clone (ST16) exhibited a low frequency of these mutations (6.0%).Analysis of 10 plasmid clusters carrying CPGs revealed the frequent co-carriage of qnrS1 (quinolone resistance) and rmtB1 (amikacin resistance).Conclusions: CRE dissemination in Southern Vietnam is driven by a dual-transmission scenario.We identified distinct CPG-linked colistin resistance pathways and significant co-carriage of qnrS1 with CPGs.This highlights the potential risk of co-selection through antibiotic pressure.These findings underscore the urgent need for surveillance strategies targeting high-risk clones like K. pneumoniae ST16.