The clinical features and genomic epidemiology of carbapenem-resistant Acinetobacter baumannii infections at a tertiary hospital in Vietnam

Abstract

Objectives: To characterise the clinical features of Acinetobacter baumannii infections and investigate the phylogenetic structure and transmission dynamics of A. baumannii in Vietnam.

Methods: Between 2019 and 2020, a surveillance of A. baumannii (AB) infections was conducted at a tertiary hospital in Ho Chi Minh City, Vietnam. Risk factors for in-hospital mortality were analysed using logistic regressions. Whole-genome sequence data were used to characterise genomic species, sequence types (STs), antimicrobial resistance genes, surface antigens, and phylogenetic relatedness of AB isolates.

Results: Eighty-four patients with AB infections were enrolled in the study, 96% of whom were hospital-acquired. Half of the AB isolates were identified from ICU-admitted patients, while the remaining isolates were from non-ICU patients. The overall in-hospital mortality was 56%, with associated risk factors including advanced age, ICU stay, exposure to mechanical ventilation/central venous catheterization, pneumonia as source of AB infection, prior use of linezolid/aminoglycosides, and AB treatment with colistin-based therapy. Nearly 91% of isolates were carbapenem-resistant; 92% were multidrug-resistant; and 6% were colistin-resistant. ST2, ST571, and ST16 were the three dominant carbapenem-resistant A. baumannii (CRAB) genotypes, exhibiting distinct AMR gene profiles. Phylogenetic analysis of CRAB ST2 isolates together with previously published ST2 collection provided evidence of intra- and inter-hospital transmission of this clone.

Conclusions: Our study highlights a high prevalence of carbapenem resistance and multidrug resistance in A. baumannii and elucidates the spread of CRAB within and between hospitals. Strengthening infection control measures and routine genomic surveillance are crucial to reducing the spread of CRAB and detecting novel pan-drug-resistant variants in a timely fashion.

Keywords: Acinetobacter baumannii; Carbapenem resistance; Hospital-acquired infections; Nosocomial infections; Whole genome sequencing.

Fig. 1

Phylogenetic structure of Acinetobacter baumannii ST2 isolates from University Medical Center, Vietnam. Maximum likelihood (ML) phylogeny of A. baumannii ST2 from University Medical Center in Ho Chi Minh City, Vietnam. The ML tree was rooted using A. baumannii ST2 strain WM99c as an outgroup. The terminal nodes are coloured according to capsular polysaccharide type (KL types) of ST2 isolates. The scale bar shows the number of SNPs. The heat map shows the presence (blue and red colour) or absence (grey colour) of acquired antimicrobial resistance genes and virulence factors.

Fig. 2

Phylogenetic structure of Acinetobacter baumannii ST2 isolates from this study together with previously published ST2 genomes from Vietnam. Maximum likelihood (ML) phylogeny of A. baumannii ST2 from this study together with previously published ST2 genomes from other hospitals in Vietnam. The ML tree is rooted using A. baumannii ST2 strain WM99c as an outgroup. The terminal nodes are coloured according to capsular polysaccharide type (KL types) of ST2 isolates. The scale bar shows the number of substitutions per site. Black stars indicate bootstrap support values ≥80% on internal nodes, with larger stars indicating higher bootstrap values. Red cross indicates clusters containing isolates from different hospitals.