Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples

Abstract

BackgroundMalonate utilization, an important differential trait, well recognized as being possessed by six of the seven Cronobacter species is thought to be largely absent in Cronobacter sakazakii (Csak). The current study provides experimental evidence that confirms the presence of a malonate utilization operon in 24 strains of sequence type (ST) 64, obtained from Europe, Middle East, China, and USA; it offers explanations regarding the genomic diversity and phylogenetic relatedness among these strains, and that of other C. sakazakii strains.ResultsIn this study, the presence of a malonate utilization operon in these strains was initially identified by DNA microarray analysis (MA) out of a pool of 347 strains obtained from various surveillance studies involving clinical, spices, milk powder sources and powdered infant formula production facilities in Ireland and Germany, and dried dairy powder manufacturing facilities in the USA. All ST64 C. sakazakii strains tested could utilize malonate. Zebrafish embryo infection studies showed that C. sakazakii ST64 strains are as virulent as other Cronobacter species. Parallel whole genome sequencing (WGS) and MA showed that the strains phylogenetically grouped as a separate clade among the Csak species cluster. Additionally, these strains possessed the Csak O:2 serotype. The nine-gene, ~ 7.7 kbp malonate utilization operon was located in these strains between two conserved flanking genes, gyrB and katG. Plasmidotyping results showed that these strains possessed the virulence plasmid pESA3, but in contrast to the USA ST64 Csak strains, ST64 Csak strains isolated from sources in Europe and the Middle East, did not possess the type six secretion system effector vgrG gene.ConclusionsUntil this investigation, the presence of malonate-positive Csak strains, which are associated with foods and clinical cases, was under appreciated. If this trait was used solely to identify Cronobacter strains, many strains would likely be misidentified. Parallel WGS and MA were useful in characterizing the total genome content of these Csak O:2, ST64, malonate-positive strains and further provides an understanding of their phylogenetic relatedness among other virulent C. sakazakii strains.Electronic supplementary materialThe online version of this article (10.1186/s13099-018-0238-9) contains supplementary material, which is available to authorized users.

Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans

“…A total of 4,523 ORFs were predicted in the genome of which 4,220 (3,959 in the chromosome) were putative protein-coding DNA sequences (CDS). These numbers are quite similar to those reported for other Cronobacter species (Chase et al, 2017;Gopinath et al, 2018;Jang et al, 2018). In addition, a total of 197 ncRNA, 7 complete rRNA operons (16S-23S-5S), one additional 5S rRNA and 84 tRNA-coding genes (82 encoding standard amino acids, 1 selenocysteine, 1 pseudogene) were predicted in the chromosome sequence, while only 2 ncRNAs were found in plasmid p2.…”

The Secretion of Toxins and Other Exoproteins of Cronobacter: Role in Virulence, Adaption, and Persistence

“…Subsequently, using in parallel a novel DNA microarray and whole genome sequencing analyses to identify Cronobacter species Gopinath et al described a nine gene malonate operon (~7.7 kbp in size) that was located between two highly conserved flanking genes, gyrB and katG in ST64 C. sakazakii strains obtained from clinical sources, foods and food production facilities in Europe, southern Asia, China, and USA [68]. Of note, the presence of gyrB and katG was also found to be conserved among all Cronobacter species even malonate-negative C. sakazakii strains of other STs; however, instead of the malonate utilization gene cluster, there is a 323-325 bp nucleotide region [68]. The under appreciation of malonate-positive C. sakazakii strains that are associated with foods presents an epidemiological problem if phenotypic identification schemes alone are used in species identity.…”

Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains

“…The strains described in this report were obtained through various surveillance studies reported by Gopinath et al [ 18 ], Jaradat et al [ 20 ], and Chon et al [ 21 ]. C. sakazakii is a Gram-negative, non-sporulating, and mesophilic, facultatively anaerobic bacterium (Kingdom Domain: Bacteria) that belongs to the phylum Proteobacteria, class Gammaproteobacteria, order Enterobacterales , within the family Enterobacteriaceae .…”

“…Moreover, linking the epidemiology of adult cases to consumption of PIF is difficult to explain [ 5 – 7 ], suggesting that there are still unknown sources, such as other foods which may be involved in causing adult infections. Although occurrences of Cronobacter species in plant- origin foods are increasingly being reported, relatively less genomic information is available [ 18 , 19 ]. Here, we describe the draft genome sequences of 26 C. sakazakii strains isolated from dried spices which were obtained from the USA, the Middle East, China, and the Republic of Korea.…”