Agrobacterium species bacteraemia, Switzerland, 2008 to 2019: a molecular epidemiological study

Abstract

Background: Agrobacterium spp. are infrequent agents of bloodstream infections linked to healthcare-associated outbreaks. However, it is unclear if outbreaks also occur across larger geographic areas. Triggered by two local clusters from putative point sources, our aim was to detect potential additional clusters in Switzerland.

Methods: We performed a nationwide descriptive study of cases in Switzerland based on a prospective surveillance system (Swiss Centre for Antibiotic Resistance, anresis.ch), from 2008 to 2019. We identified patients with Agrobacterium spp. isolated from blood cultures and used a survey to collect clinical-epidemiological information and susceptibility testing results. We performed whole genome sequencing (WGS) of available clinical isolates and determined their relatedness by single nucleotide polymorphism (SNP) variant calling analysis.

Results: We identified a total of 36 cases of Agrobacterium spp. from blood samples over 10 years. Beyond previously known local clusters, no new ones were identified. WGS-based typing was performed on 22 available isolates and showed no clonal relationships between newly identified isolates or to those from the known clusters, with all isolates outside these clusters being at least 50 SNPs apart.

Conclusion and relevance: Agrobacterium spp. bacteraemia is infrequently detected and, given that it may be healthcare-associated and stem from a point source, occurrence of multiple episodes should entail an outbreak investigation. With the help of the national antimicrobial resistance surveillance system we identified multiple clinical cases of this rare pathogen but found no evidence by WGS that suggested a nation-wide outbreak.

Keywords: Agrobacterium species; Nosocomial; Outbreak; WGS.

Fig. 1

Flowchart of included cases and sequenced isolates

Fig. 2

Overview of the 36 cases. We plotted the number of annual cases (x-axis) for all healthcare institutions (y-axis; 1–10) of Agrobacterium spp. bacteraemia and indicated availability for whole genome sequencing. Indicated are the initial presumptive species identifications by the originating microbiology laboratories, which may differ from the definite identification by WGS as shown in Fig. 3

Fig. 3

TYGS genome comparison of 20 of the 22 sequenced isolates compared to reference genomes. Isolates described in this paper are shown with blue + , including the previously described isolates [11] from the two clusters at Institution 6 (AGRBE03_C, AGRBE05_E & AGRBE06_F and ARGREBE01_A) with a green + . AGREBE02_B and AGRBE04_D were excluded from this analysis, as they are identical to AGREBE02_A and AGRBE04_C respectively. Species clusters are marked by colours, using 70% dDDH cutoffs