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. 2014 Dec 16;15(1):1121.
doi: 10.1186/1471-2164-15-1121.

Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis

Stephen J Forsythe  1 , Benjamin Dickins, Keith A Jolley
Affiliations

Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis

Stephen J Forsythe et al. BMC Genomics. .

Abstract

Background: Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 requested the establishment of a molecular typing scheme to enable the international control of the organism. This paper presents the application of Next Generation Sequencing (NGS) to Cronobacter which has led to the establishment of the Cronobacter PubMLST genome and sequence definition database (http://pubmlst.org/cronobacter/) containing over 1000 isolates with metadata along with the recognition of specific clonal lineages linked to neonatal meningitis and adult infections

Results: Whole genome sequencing and multilocus sequence typing (MLST) has supports the formal recognition of the genus Cronobacter composed of seven species to replace the former single species Enterobacter sakazakii. Applying the 7-loci MLST scheme to 1007 strains revealed 298 definable sequence types, yet only C. sakazakii clonal complex 4 (CC4) was principally associated with neonatal meningitis. This clonal lineage has been confirmed using ribosomal-MLST (51-loci) and whole genome-MLST (1865 loci) to analyse 107 whole genomes via the Cronobacter PubMLST database. This database has enabled the retrospective analysis of historic cases and outbreaks following re-identification of those strains.

Conclusions: The Cronobacter PubMLST database offers a central, open access, reliable sequence-based repository for researchers. It has the capacity to create new analysis schemes 'on the fly', and to integrate metadata (source, geographic distribution, clinical presentation). It is also expandable and adaptable to changes in taxonomy, and able to support the development of reliable detection methods of use to industry and regulatory authorities. Therefore it meets the WHO (2004) request for the establishment of a typing scheme for this emergent bacterial pathogen. Whole genome sequencing has additionally shown a range of potential virulence and environmental fitness traits which may account for the association of C. sakazakii CC4 pathogenicity, and propensity for neonatal CNS.

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Figures

Figure 1
Figure 1
Maximum likelihood tree of the seven multilocus sequence typing loci (3036 base pair concatenated length) for the members of Cronobacter genus and closely related Franconibacter and Siccibacter genera. The tree was drawn using MEGA 6.05 (http://www.megasoftware.net/) with 1000 bootstrap replicates.
Figure 2
Figure 2
Population snapshot of the Cronobacter MLST database generated using the GoeBURST algorithm, indicating the clonal complexes and the diversity of the sources of the strains. The threshold for the output was set to triple locus variation. The dominant STs are represented by the circles with larger diameters. From Joseph & Forsythe, 2012.
Figure 3
Figure 3
7-loci Splits Network of 298 sequence types from the Cronobacter genus. (a) Analyis of the whole Cronobacter genus (b) Analysis of C. sakazakii and C. malonaticus.
Figure 4
Figure 4
rMLST analysis of genomes across the Cronobacter , Franconibacter and Siccibacter genera.
Figure 5
Figure 5
COG-cgMLST analysis of Cronobacter sakazakii genomes. 7-loci MLST sequence types highlighted.
See this image and copyright information in PMC

References

    1. Maiden MC, van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. MLST revisited: The gene-by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013;11:728–736. doi: 10.1038/nrmicro3093. - DOI - PMC - PubMed
    1. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FH, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MCJ. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiol. 2012;158:1005–1015. doi: 10.1099/mic.0.055459-0. - DOI - PMC - PubMed
    1. Jolley KA, Maiden MC. Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar. Euro Surveill. 2013;18:pii=20379. - PMC - PubMed
    1. Sheppard SK, Jolley KA, Maiden MJC. A gene-by-gene approach to bacterial population genomics: whole genome MLST of Campylobacter. Genes. 2012;3:261–277. doi: 10.3390/genes3020261. - DOI - PMC - PubMed
    1. Pérez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA. Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect Gen Evol. 2013;16:38–53. doi: 10.1016/j.meegid.2013.01.009. - DOI - PubMed

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