Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing

Abstract

BackgroundA number of episodes of nosocomial Agrobacterium spp. bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation.MethodsCases of Agrobacterium spp. bacteremias that occurred between August 2011 and February 2017 were investigated employing line lists, environmental sampling, rapid protein- (MALDI-TOF MS), and genome-based typing (pulsed field gel electrophoresis and whole genome sequencing) of the clinical isolates.ResultsWe describe a total of eight bacteremia episodes due to A. radiobacter (n = 2), Agrobacterium genomovar G3 (n = 5) and A. pusense (n = 1). Two tight clusters were observed by WGS typing, representing the two A. radiobacter isolates (cluster I, isolated in 2015) and four of the Agrobacterium genomovar G3 isolates (cluster II, isolated in 2016 and 2017), suggesting two different point sources. The epidemiological investigations revealed two computer tomography (CT) rooms as common patient locations, which correlated with the two outbreak clusters. MALDI-TOF MS permitted faster evaluation of strain relatedness than DNA-based methods. High resolution WGS-based typing confirmed the MALDI-TOF MS clustering.ConclusionsWe report clinical and epidemiological characteristics of two outbreak clusters with Agrobacterium. spp. bacteremia likely acquired during CT contrast medium injection and highlight the use of MALDI-TOF MS as a rapid tool to assess relatedness of rare gram-negative pathogens in an outbreak investigation.

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

“…The mean coverage for each sample was in excess of 47x. Assemblies were generated using Unicycler v0.4.8 [18] and used in Genometo-Genome Distance Calculator (GGDC) [19] for digital DNA:DNA hybridization (dDDH) species determination against the panel of reference isolates described [11] using 70% cutoff (formula 2). A comparison of genomes was generated in the Type (Strain) Genome Server (TYGS) [20].…”

“…22 isolates from five healthcare institutions were sequenced (Fig. 2): eight from the initial outbreak investigations [11] and 14 additional isolates as part of this study. This accounts for 61% (22/36) of the cases included.…”

“…From 2011-2017, a series of eight patients with Agrobacterium spp. bacteraemia was noted at Bern University Hospital [11]. All of these patients had previously undergone a CT scan and had received intravenous contrast medium.…”

“…This suggested a common transmission pathway with introduction from two different point sources. Despite an extensive outbreak investigation, the sources could not be identified [11].…”

NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology

“…Such studies have found that 9% of intensive care unit bloodstream isolates may be from clonal lineages [ 6 ], that endoscopes are commonly identified as potential vectors of transmission events in patients undergoing endoscopy [ 44 , 45 ], and that lapses in contrast preparation and injection can be the cause of vancomycin-resistant enterococci and Agrobacterium spp. outbreaks in patients undergoing radiological studies or interventions [ 46 , 47 ]. Donor-derived bacterial infections have been traced to solid organ transplants in the case of Mycobacterium hominis and a variety of antibiotic-resistant organisms [ 48–50 ].…”