Molecular Epidemiology and Clone Transmission of Carbapenem-Resistant Acinetobacter baumannii in ICU Rooms

Abstract

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause of nosocomial infections and hospital outbreaks worldwide, remaining a critical clinical concern. Here we characterized and investigated the phylogenetic relationships of 105 CRAB isolates from an intensive care unit from one hospital in China collected over six years. All strains carried bla_OXA-23 , bla_OXA-66 genes for carbapenem resistance, also had high resistance gene, virulence factor, and insertion sequence burdens. Whole-genome sequencing revealed all strains belonged to ST2, the global clone CC2. The phylogenetic analysis based on the core genome showed all isolates were dominated by a single lineage of three clusters and eight different clones. Two clones were popular during the collection time. Using chi-square test to identify the epidemiologically meaningful groupings, we found the significant difference in community structure only existed in strains from separation time. The haplotype and median-joining network analysis revealed genetic differences appeared among clusters and changes occurred overtime in the dominating cluster. Our results highlighted substantial multidrug-resistant CRAB burden in the hospital ICU environment demonstrating potential clone outbreak in the hospital.

Keywords: Acinetobacter baumannii; carbapenem-resistant; clone spread; nosocomial infection; whole-genome sequencing.

Figure 1

Spatiotemporal, demographic, and clinical characteristics of 105 isolates of Shunde hospital. (A–C) Sample distribution from male patients; (D–F) Sample distribution from female patients; the sampling time range was 2013–2018, and the patients were divided into four groups according to age: 0–10 years old, 10–40 years old, 40–65 years old and over 65 years old. The sampling source was divided into three groups: blood, sputum, and other secretions.

Figure 2

Results of pan-genomic analysis. (A) Matrix with the presence and absence of core and accessory genes. A total of 9,506 genes were clustered and annotated with different colors. different clonalities based on SNP distance and different clusters based on bayesian classification. (B) Pie chart shows different kinds of accessory genes; the number of core genes was 3,202.

Figure 3

Maximum likelihood phylogenetic trees from core genome alignments of CRAB isolates. Phylogenetic tree constructed from the core genomic file excluding the standard strain M19606; colored annotations are added next to the main tree for sampling time and sources, patient ages and genders and cluster and clonality classification of 105 CRAB isolates.

Figure 4

The scatter plots of SNP distance reduced dimension among CRAB isolates. The SNP distance matrix is standardized by R function scale and then the function dist (method = “euclidean”) is used to calculate the distance between variables. The results are visualized by using the function cmdscale and by Package ggplot2.

Figure 5

Distribution of CRAB clonalities in different spatial temporal, demographic, and clinical characteristics. (A) Distribution of CRAB clonalities in different sampling sources. (B) Distribution of CRAB clonalities in different sampling years. (C) Distribution of CRAB clonalities in different patient ages. (D) Distribution of CRAB clonalities in different patient genders.

Figure 6

Evolutionary relationships and geographical distribution of 55 haplotypes of 105 isolates from Shunde hospital. (A) Circle colors represent different clusters based on bayesian classification. (B) Circle colors represent different clonalities based on SNP distance. (C) Circle colors represent sampling time. The density of those bars represents the genetic distance between the haplotypes; circle sizes represent the number of isolates in a haplotype.

Figure 7

Mismatch distribution analyses of coding region alignment of 105 genomes from Shunde hospital. (A–C) Results of Mismatch distribution analyses by Alrequin. (D–F) Results of Mismatch distribution analyses by DnaSP.

Figure 8

MIC test and ARGs, virulence genes (VGs), insertion sequence (IS) identification of 105 samples from ICU rooms. (A) Results of MIC test; class of antibiotics and resistance strength are annotated as colored bars next to the main heatmap. (B) Results of ARG identification based on Resfinder; (C) Results of IS based on ISfinder; (D) Results of VG identification based on VFDB.