sakazakii and 16 C. malonaticus strains. To assess the performance of the MLST scheme, Cronobacter strains were selected to be representative of the different biotypes (most of which were previously derived in an earlier study [3]), and were also distributed both temporally and geographically in terms of their isolation (See Additional file 1). In silico sequence

data was also obtained for all the loci from C. sakazakii strain ATCC BAA-894 (Accession No. CP000785), Citrobacter koseri strain ATCC BAA-895 (Accession No. CP000822), and Enterobacter species strain 683 (Accession No. CP000653). The latter strain sequence data was used to root the data set. The seven alleles obtained for the C. sakazakii genome reference strain BAA-894

were identical to the online genome sequence (CP000785). The mean allele length was 434 bp for the scheme and ranged between 363 bp (glnS) and 507 bp (gltB) in length (Table 2). All alleles within ATM inhibitor a particular locus were found to be of an identical length for all Cronobacter strains examined. Angiogenesis inhibitor Nucleotide sequence diversity at all seven loci is shown in Table 2. The proportion of variable sites varied from 10.8% (atpD) to 27.6% (gyrB) which extended over the whole section of the sequenced allele. Table 2 Analysis of the seven MLST loci in the Cronobacter strains sampled. Gene Size (bp) of fragment analysed No. of alleles No. of polymorphic sites Proportion of fragment this website as polymorphic sites (%) d N /d S atpD 390 12 42 10.8

0.006 fusA 438 12 69 15.8 0.061 glnS 363 12 72 19.8 0.062 gltB 507 11 118 23.3 0.059 gyrB 402 13 111 27.6 0.055 infB 441 12 87 19.7 0.079 Pps 495 15 123 24.8 0.033 Allele variation is not necessarily equally likely at every nucleotide of each locus. If a locus does not have a role affected by a selective pressure (such as antibiotic exposure) then nucleotide substitutions would frequently not be expected to change the amino acid sequence (synonymous) as changes are likely to be eliminated by purifying selection. By calculating the d N /d S ratio Selleckchem Vorinostat (non-synonymous substitutions to synonymous substitutions) the degree of selection operating on each locus can be estimated. The d N /d S ratio for all seven loci within Cronobacter strains was found to be significantly less than 1, ranging from 0.006 (atpD) to 0.079 (infB) (Table 2), indicating that no strong positive selective pressure was present at any of the loci selected, validating their suitability for inclusion in the MLST scheme. Assignment of allele and sequence types The number of different alleles resolved from this Cronobacter MLST scheme at each locus ranged from 11 (gltB) to 15 (pps) alleles. The mean number of allele types per locus was found to be 13.4, providing the potential to distinguish >7 × 1010 different genotypes and also making it highly unlikely to obtain identical sequence types (ST) by chance.