Characterization of Cronobacter spp. isolated from food products in Poland and comparative genomic analysis of Cronobacter sakazakii isolate MK_10 and a clinical strain associated with a fatal neonatal infection

<i>Cronobacter</i> spp. are ubiquitous environmental bacteria associated with infections affecting all age groups, with infants and elderly individuals particularly at risk. We investigated the prevalence of <i>Cronobacter</i> spp. in 251 food samples collected in Poland, including raw milk, powdered milk, infant formula, dried herbs and spices, dried teas, and raw vegetables. <i>Cronobacter</i> strains were isolated from 26 samples (10.4%) and classified into five species: <i>C. sakazakii</i>, <i>C. muytjensii</i>, <i>C. turicensis</i>, <i>C. malonaticus</i> and <i>C. dublinensis</i>. The isolates were grouped based on sequence variation of the <i>fusA</i> and <i>rpoB</i> genes, and further differentiated according to their biochemical profiles. The complete nucleotide sequence of <i>C. sakazakii</i> MK_10, a plasmid-rich strain isolated from dried oregano and representing the most prevalent species in the collected strain pool, was obtained. Comparative genomic analysis of MK_10, the first fully sequenced foodborne <i>C. sakazakii</i> strain in Poland, with a clinical strain from a fatal neonatal case revealed the presence of a conserved set of genes associated with pathogenic properties. MK_10 carries three extrachromosomal replicons, including two IncFIB plasmids - pCS-MK10_P1 (114 kb), representing the pESA3 family of virulence plasmids, and pCS-MK10_P2 (45.9 kb) carrying a copper homeostasis and silver resistance island (CHASRI). Comparative analyses revealed that the structure of the MK_10 chromosome has been shaped by multiple insertion and deletion events, associated mainly with prophages (e.g., a novel intact prophage related to <i>Cronobacter</i> phage ENT47670) and other integrative elements. The MK_10 genome contains only two transposable elements: an isoform of insertion sequence IS<i>Ehe2</i> (IS<i>3</i> family) and a non-autonomous Tn<i>3</i>-family transposon of unique structure - both located within two functional integrative elements (IE), designated IE<i>Csak_MK101</i> (32.3 kb) and IE<i>Csak_MK102</i> (32.4 kb). The identified mobile genetic elements, plasmids, and IEs, harbor genes of adaptive value, which potentially contribute to the strain's environmental fitness and pathogenic potential.