Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands

Abstract

Acinetobacter baumannii is a nosocomial pathogen that frequently causes healthcare-acquired infections. The global spread of multidrug-resistant (MDR) strains with its ability to survive in the environment for extended periods imposes a pressing public health threat. Two MDR A. baumannii outbreaks occurred in 2012 and 2014 in a companion animal intensive care unit (caICU) in the Netherlands. Whole-genome sequencing (WGS) was performed on dog clinical isolates (n = 6), environmental isolates (n = 5), and human reference strains (n = 3) to investigate if the isolates of the two outbreaks were related. All clinical isolates shared identical resistance phenotypes displaying multidrug resistance. Multi-locus Sequence Typing (MLST) revealed that all clinical isolates belonged to sequence type ST2. The core genome MLST (cgMLST) results confirmed that the isolates of the two outbreaks were not related. Comparative genome analysis showed that the outbreak isolates contained different gene contents, including mobile genetic elements associated with antimicrobial resistance genes (ARGs). The time-measured phylogenetic reconstruction revealed that the outbreak isolates diverged approximately 30 years before 2014. Our study shows the importance of WGS analyses combined with molecular clock investigations to reduce transmission of MDR A. baumannii infections in companion animal clinics.

Keywords: Acinetobacter baumannii; antimicrobial resistance; veterinary medicine; whole-genome sequencing.

Figure 1

Outbreak investigation of MDR A. baumannii isolates in companion animal intensive care unit (caICU) in the Netherlands using cgMLST. (A) The minimum spanning tree of A. baumannii isolates is based on 2390 target genes of core genome MLST (cgMLST). The nodes are colored by complex types (CT) provided by cgMLST. Isolate IDs are labeled in the nodes, and the numbers between each circle indicate the cgMLST SNP differences between the isolates. The highlighted clonal clusters represent closely related genotypes (≤10 different alleles). (B) An epidemic curve of A. baumannii infections in which different colors correspond to different complex types (CT).

Figure 2

The differences in gene content between genomes included in this study. The pan-genomic matrix (right block) shows the absence and presence of core and accessory genes corresponding to mid-rooted phylogenetic dendrogram (left) (blue = presence of genes, white = absence of genes). The red line (top) indicates the size of contigs with different kilobase (kb). The blue line curve underneath the matrix displays the frequency of the presence of genes in each genome.

Figure 3

The presence and absence of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) associated with ARGs in genomes included in this study. The isolation source was represented by colored squares (red = human, blue = dog, black = environment). The colored circles indicated the presence of genes in which different colors showed different classes of ARGs (purple = aminoglycosides, red = beta-lactam, yellow = tetracyclines, black = sulfonamides, green = chloramphenicol), antiseptic (dark green = quaternary ammonium compound-resistant protein, qacE), dfrA5 (light grey) and efflux pumps (AdeABC), and MGEs colored in cyan.