Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit

Masood, N., Moore, K., Farbos, A., Paszkiewicz, K., Dickins, B. ORCID: 0000-0002-0866-6232, McNally, A. ORCID: 0000-0002-3099-630X and Forsythe, S. ORCID: 0000-0002-6709-0712, 2015. Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit. BMC Genomics, 16. ISSN 1471-2164

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Background: Cronobacter sakazakii is a member of the genus Cronobacter that has frequently been isolated from powdered infant formula (PIF) and linked with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. The Cronobacter MLST scheme has reported over 400 sequence types and 42 clonal complexes; however C. sakazakii clonal complex 4 (CC4) has been linked strongly with neonatal infections, especially meningitis. There have been a number of reported Cronobacter outbreaks over the last three decades. The largest outbreak of C. sakazakii was in a neonatal intensive care unit (NICU) in France (1994) that lasted over 3 months and claimed the lives of three neonates. The present study used whole genome sequencing data of 26 isolates obtained from this outbreak to reveal their relatedness. This study is first of its kind to use whole genome sequencing data to analyse a Cronobacter outbreak. Methods: Whole genome sequencing data was generated for 26 C. sakazakii isolates on the Illumina MiSeq platform. The whole genome phylogeny was determined using Mugsy and RaxML. SNP calls were determined using SMALT and SAMtools, and filtered using VCFtools. Results: The whole genome phylogeny suggested 3 distant clusters of C. sakazakii isolates were associated with the outbreak. SNP typing and phylogeny indicate the source of the C. sakazakii could have been from extrinsic contamination of reconstituted infant formula from the NICU environment and personnel. This pool of strains would have contributed to the prolonged duration of the outbreak, which was up to 3 months. Furthermore 3 neonates were co-infected with C. sakazakii from two different genotype clusters. Conclusion: The genomic investigation revealed the outbreak consisted of an heterogeneous population of C. sakazakii isolates. The source of the outbreak was not identified, but probably was due to environmental and personnel reservoirs resulting in extrinsic contamination of the neonatal feeds. It also indicated that C. sakazakii isolates from different genotype clusters have the ability to co-infect neonates.

Item Type: Journal article
Publication Title: BMC Genomics
Creators: Masood, N., Moore, K., Farbos, A., Paszkiewicz, K., Dickins, B., McNally, A. and Forsythe, S.
Publisher: BioMed Central Ltd.
Date: 2015
Volume: 16
ISSN: 1471-2164
Rights: © 2015 Masood et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
Divisions: Schools > School of Science and Technology
Record created by: Jonathan Gallacher
Date Added: 06 Nov 2015 11:10
Last Modified: 09 Jun 2017 13:56

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