title: Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
authors.forename: Naqash
authors.initials: N
authors.lastname: Masood
authors.affiliation: Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, EX4 4QD, Exeter, UK.
authors.forename: Karen
authors.initials: K
authors.lastname: Moore
authors.affiliation: Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, EX4 4QD, Exeter, UK.
authors.forename: Audrey
authors.initials: A
authors.lastname: Farbos
authors.affiliation: Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, EX4 4QD, Exeter, UK.
authors.forename: Konrad
authors.initials: K
authors.lastname: Paszkiewicz
authors.affiliation: Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Dickins
authors.affiliation: Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
authors.forename: Alan
authors.initials: A
authors.lastname: McNally
authors.affiliation: Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK. stephen.forsythe@ntu.ac.uk.
authors.forename: Stephen
authors.initials: S
authors.lastname: Forsythe
mesh_terms: D044083:Cronobacter sakazakii / Q000145:classification / Q000235:genetics*; D003428:Cross Infection; D004196:Disease Outbreaks; D004756:Enterobacteriaceae Infections / Q000453:epidemiology* / Q000266:history / Q000382:microbiology*; D005602:France / Q000453:epidemiology; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D049673:History, 20th Century; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007363:Intensive Care Units, Neonatal; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide