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Multiple disease outbreaks of <jats:italic>C. sakazakii<\/jats:italic> have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of <jats:italic>C. sakazakii<\/jats:italic> and 48 genomes of related <jats:italic>Cronobacter<\/jats:italic> species isolated from diverse sources.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The <jats:italic>C. sakazakii<\/jats:italic> pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes <jats:italic>fos<\/jats:italic> which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and <jats:italic>mdf(A)<\/jats:italic> which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of <jats:italic>C. sakazakii<\/jats:italic> within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for <jats:italic>Cronobacter<\/jats:italic>-related diseases.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-019-1664-7","type":"journal-article","created":{"date-parts":[[2019,12,27]],"date-time":"2019-12-27T17:02:58Z","timestamp":1577466178000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle"],"prefix":"10.1186","volume":"19","author":[{"given":"Isaiah Paolo A.","family":"Lee","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4428-0924","authenticated-orcid":false,"given":"Cheryl P.","family":"Andam","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,12,27]]},"reference":[{"key":"1664_CR1","doi-asserted-by":"publisher","first-page":"5368","DOI":"10.1128\/JCM.42.11.5368-5370.2004","volume":"42","author":"C Iversen","year":"2004","unstructured":"Iversen C, Waddington M, On SLW, Forsythe S. 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