A more detailed examination of the strains allocated to each cluster showed that all strains labelled as pathogenic were positive for the inositol fermentation (Ino) test, whilst Bioactive Compound Library screening the prospective non-pathogenic strains were negative for this test. Although this is not conclusively shown by the result of the Inositol test
in Test 1 and Test 2, the Test 1 data does indicate a bias towards strains with inositol fermentation in the pathogenic cluster. This suggested that either inositol fermentation was a requirement for pathogenicity, or that the genetic locus conferring inositol fermentation was linked to genes conferring pathogenic traits. This latter conclusion was supported by the two check details apparently pathogenic ST 4 strains which were negative for inositol fermentation (strains 552 and 553): strain 552 was isolated from infant formula, but strain 553 was associated with neonatal meningitis indicating pathogenesis. It is probable that the inositol fermentation gene was lost from these strains, but the pathogenic traits acquired alongside it remained. It should be noted that this test is different from the INO test in the Test 2 dataset, which we removed from the analysis as it produces
the same result for all Cronobacter strains. Table 4 Clusters from Test 4 dataset Cronobacter species MLST Type Cluster 1: potential non-pathogenic Source(number of strains) Cluster 2: potential pathogenic Source (number https://www.selleckchem.com/products/lazertinib-yh25448-gns-1480.html of strains) C. sakazakii 1 IF(5), C(1), Faeces(1) C. sakazakii 3 IF(1), EFT(2), FuF(4), WF(1), U(1) C. sakazakii 4 C(1), IF(1) C(8), IF(6), MP(1), WF(1), E(1), Washing Brush(1), U(2) C. sakazakii 8 C(7), IF(1) C. sakazakii 9 WF(1) C. sakazakii 12 C(1) C(2), WF(1), U(1) C. sakazakii 13 IF(1), C(1) C. sakazakii 14 IF(1) C. sakazakii 15 C(1) C. sakazakii 16 Spices(1) C. sakazakii 17 IF(1) C. sakazakii 18 C(1) C. malonaticus 7 C(6), F(1), WF(1), Amine dehydrogenase Faeces(1) C(1), MP(1) C. malonaticus 10 Herbs(2) C. malonaticus 11 C(2) C(1) All strains in cluster 1 (non-pathogenic) are
negative for inositol fermentation, all strains in cluster 2 are positive for inositol fermentation. For abbreviations in this table see footnote to Table 1. Sources of isolation and strain numbers are given in full in Additional File 1. Consensus Clustering Aggregating the clustering assignments based on the majority rule (two out of four) for the 48 strains which have data available from all four tests resulted in the clusters shown in Table 5. The results showed the majority of ST 4 strains were placed in cluster 2. However, there was still splitting of ST 1, 3 and 7 strains between the two clusters. There were also only 10 of the 48 strains placed in the non-pathogenic category. It was hypothesised that the results from Test 2 could be skewing the results, as this test did not differentiate between strains of different MLST sequence types.