Table 1.
General features, sources, malonate reaction, and genomic attributes of the strains used in this study
| Strain | Source (isolation date) | Malonate utilizeda | Serotype | Sequence type | Clonal complex | Draft genome size (bp) | G+C content (%) | Contigs | CDS | NCBI accession no. |
|---|---|---|---|---|---|---|---|---|---|---|
| 7405-71-1A (Comp 11) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,432,172 | 56.74 | 124 | 4104 | NHQL00000000 |
| 7405-68-2 (Comp 19) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,537,591 | 56.85 | 121 | 4205 | NHQM00000000 |
| 7405-71-1B (Comp 20) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,564,009 | 56.77 | 190 | 4228 | NEXY00000000 |
| 867009 DFI106-1 (Comp 45) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,731,392 | 56.8 | 117 | 4213 | NEXZ00000000 |
| 867009 RF106-1 (Comp 46) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,728,640 | 56.77 | 107 | 4407 | NEYA00000000 |
| 7405-80-2 (Comp 49) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,498,706 | 56.9 | 108 | 4159 | NEYB00000000 |
| 7405-68-4 (Comp 53) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,545,852 | 56.8 | 101 | 4,177 | NEYC00000000 |
| 7405-75-1 (Comp 54) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,540,274 | 57 | 135 | 4210 | NEYD00000000 |
| 7405-75-2 (Comp 57) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,538,462 | 56.8 | 101 | 4200 | NEYE00000000 |
| 0210ELJ 72-1 (Comp 59) | Environmental, compliance activity (2014), USA | (+) | Csak O:2 | 64 | 64 | 4,649,928 | 56.5 | 173 | 4310 | NEYF00000000 |
| CDC 1121-73c | Human, clinical Bronchial. wash (1973), USA | (+) | Csak O:2 | 64 | 64 | 4,443,589 | 57 | 238 | 4112 | MCOD00000000 |
| GK 1025c | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | 64 | 64 | 4,599,266 | 56.7 | 94 | 4295 | MCOE00000000 |
| GK 1026 | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | 64 | 64 | 4,603,121 | 56.73 | 126 | 4298 | NEYG00000000 |
| GK 1027 | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | 64 | 64 | 4,603,249 | 56.7 | 34 | 4304 | NHQN00000000 |
| GK 1028 | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | ND | ND | ND | ND | ND | ND | Not Yet Submitted |
| GK 1029 | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | 64 | 64 | 4,589,912 | 56.7 | 95 | 4292 | NHQO00000000 |
| GK 1030 | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | 64 | 64 | 4,601,082 | 56.7 | 37 | 4286 | NHQP00000000 |
| GK 1034 | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | 64 | 64 | 4,604,244 | 56.7 | 29 | 4296 | NHQQ00000000 |
| GK 1035 | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | 64 | 64 | 4,597,230 | 56.7 | 50 | 4282 | NHQR00000000 |
| GK 1326 | Environmental, PIF manufacturing facility (2015), Germany | (+) | Csak O:2 | 64 | 64 | 4,423,544 | 56.73 | 153 | 4096 | NEYH00000000 |
| E772 | Milk powder, France | (+) | Csak O:2 | 64 | 64 | 4,537,187 | 56.8 | 351 | 4163 | NHQS00000000 |
| H169/1/16 | Environmental, PIF manufacturing facility (2012), Switz | (+) | Csak O:2 | 64 | 64 | 4,474,959 | 57 | 32 | 4139 | NHTV00000000 |
| Jor172 | Food, spices, Jordan | (+) | Csak O:2 | 64 | 64 | 4,330,450 | 57 | 25 | 4000 | NCWD00000000 |
| Cro2819A3c | Mushroom (2017), China | ND | ND | 64 | 64 | 4,725, 000 | 57.2 | 168 | 3994 | NZMBSC00000000 |
| C. universalis NCTC9529T | Water, (1956), UK | (+) | Cuni O:1 | 54 | Unknownb | 4,388,239 | 55.79 | 16 | 3977 | CAKX00000000 |
| C. condimenti LMG26250T | Fermented spiced sausage, (2010), Slovakia | (+) | Unknown | 98 | Unknownb | 4,480,620 | 55.8 | 155 | 4169 | CAKW00000000 |
| C. dublinensis LMG23823T | Environmental, milk powder manufacturing plant (2004), Ireland | (+) | Cdub O:1 | 106 | Unknownb | 4,644,913 | 56.16 | 41 | 4172 | CP012266 |
| C. malonaticus LMG23826T | Clinical, breast abscess (1977), USA | (+) | Cmal O:2 | 7 | 7 | 4,419,871 | 54.9 | 69 | 4041 | CP013940 |
| C. turicensis LMG23827T | Clinical, blood (2005), Switzerland | (+) | Ctur O:1 | 19 | 24 | 4,599,092 | 57.2 | 1 | 4296 | FN543093 |
| C. muytjensii 51329T | Unknown, USA | (+) | Cmuy O:2 | 81 | 81 | 4,355,922 | 56.17 | 32 | 3973 | CP012268 |
| C. sakazakii BAA-894 | Infant formula (2001), USA | (−) | Csak O:1 | 1 | 1 | 4,530,777 | 56.7 | 4211 | CP000783 |
Cronobacter species identities were established using the species-specific rpoβ PCR assay as described by Stoop et al. [23] and Lehner et al. [24], and the cgcA species-specific PCR assay as described by Carter et al. [20]. Moreover, serotyping was assigned using the molecular-based serogrouping scheme described by Yan et al. [21], the results of which confirmed results of the rpoβ- and cgcA-based PCR species identification assays for each strain
ND not determined
aMalonate utilization was performed using Ewing Modified Malonate Broth according to the original assay described by Leifson [28] and modified by Ewing et al. [29]. Results were summarized after 48 h incubation at 37 °C
bNo clonal complex was found for this strain in the Cronobacter MLST database
cC. sakazakii strain Cro2819A3 was submitted to NCBI by Zeng et al. [27], and strains 1025 and 1121-73 were previously reported by Chase et al. [18]